RosaBioinfo

Comparison of flye assemblies with different parameters

Maxime Mahout, Blandine Trouche 2026-05-27

Comparison of flye assemblies with different parameters

Our original assembly

Our original assembly uses options --meta and --nano-raw.

flye --nano-raw 00_RAW_DATA/Cel_g3_SUP_noCulex.fastq.gz \
     --out-dir 02_ASSEMBLY_onlybac --meta 

grep -F -e "root: INFO:" -e "DEBUG: Cmd:" -e "  Total" -e " Fragments" -e " Mean cov" 02_ASSEMBLY_onlybac/flye.log

## [2024-07-01 17:16:27] root: INFO: Starting Flye 2.9.1-b1780
## [2024-07-01 17:16:27] root: DEBUG: Cmd: /Users/btrouche/opt/miniconda3/envs/flye/bin/flye --nano-raw 00_RAW_DATA/Cel_g3_SUP_noCulex.fastq.gz --out-dir 02_ASSEMBLY_onlybac --meta
## [2024-07-01 17:16:27] root: INFO: >>>STAGE: configure
## [2024-07-01 17:16:27] root: INFO: Configuring run
## [2024-07-01 17:16:28] root: INFO: Total read length: 63028141
## [2024-07-01 17:16:28] root: INFO: Reads N50/N90: 2979 / 566
## [2024-07-01 17:16:28] root: INFO: Minimum overlap set to 1000
## [2024-07-01 17:16:28] root: INFO: >>>STAGE: assembly
## [2024-07-01 17:16:28] root: INFO: Assembling disjointigs
## [2024-07-01 17:21:17] root: INFO: >>>STAGE: consensus
## [2024-07-01 17:21:17] root: INFO: Running Minimap2
## [2024-07-01 17:21:51] root: INFO: Computing consensus
## [2024-07-01 17:22:36] root: INFO: Alignment error rate: 0.089411
## [2024-07-01 17:22:36] root: INFO: >>>STAGE: repeat
## [2024-07-01 17:22:36] root: INFO: Building and resolving repeat graph
## [2024-07-01 17:23:24] root: INFO: >>>STAGE: contigger
## [2024-07-01 17:23:24] root: INFO: Generating contigs
## [2024-07-01 17:23:25] root: INFO: >>>STAGE: polishing
## [2024-07-01 17:23:25] root: INFO: Polishing genome (1/1)
## [2024-07-01 17:23:25] root: INFO: Running minimap2
## [2024-07-01 17:23:57] root: INFO: Separating alignment into bubbles
## [2024-07-01 17:24:44] root: INFO: Alignment error rate: 0.057533
## [2024-07-01 17:24:44] root: INFO: Correcting bubbles
## [2024-07-01 17:26:35] root: INFO: >>>STAGE: finalize
## [2024-07-01 17:26:35] root: INFO: Assembly statistics:
##  Total length:   1605228
##  Fragments:  32
##  Fragments N50:  1186786
##  Mean coverage:  33
## [2024-07-01 17:26:35] root: INFO: Final assembly: /Users/btrouche/Desktop/Bioinformatique/RosaBioinfo/Celg3_Long_reads/02_ASSEMBLY_onlybac/assembly.fasta

After removal of 8 non-Wolbachia contigs with anvi’o, we obtain the following genome:

cd CelG_Assembly/ && grep ">" assembly.fasta -c; echo "(number of contigs)" && cd ..

## 24
## (number of contigs)

For easy visualization of contig lengths and GC content, we use the custom script provided here: sequence_lengths.py

cd CelG_Assembly/ && /home/mmahout/miniforge3/bin/python sequence_lengths.py && cd ..

## Sequence ID: contig_2    Length: 1186930 GC Content: 34.07%
## Sequence ID: contig_23   Length: 17160   GC Content: 36.08%
## Sequence ID: contig_3    Length: 112962  GC Content: 34.57%
## Sequence ID: contig_24   Length: 10766   GC Content: 33.81%
## Sequence ID: contig_10   Length: 41477   GC Content: 33.92%
## Sequence ID: contig_9    Length: 18485   GC Content: 35.54%
## Sequence ID: contig_15   Length: 5040    GC Content: 33.13%
## Sequence ID: contig_13   Length: 7964    GC Content: 33.31%
## Sequence ID: contig_7    Length: 12018   GC Content: 35.50%
## Sequence ID: contig_22   Length: 38879   GC Content: 34.59%
## Sequence ID: contig_14   Length: 29058   GC Content: 34.98%
## Sequence ID: contig_5    Length: 731 GC Content: 33.93%
## Sequence ID: contig_19   Length: 2788    GC Content: 36.48%
## Sequence ID: contig_38   Length: 5948    GC Content: 33.42%
## Sequence ID: contig_6    Length: 1288    GC Content: 33.62%
## Sequence ID: contig_17   Length: 4007    GC Content: 36.76%
## Sequence ID: contig_1    Length: 3109    GC Content: 35.70%
## Sequence ID: contig_20   Length: 1274    GC Content: 34.14%
## Sequence ID: contig_27   Length: 1953    GC Content: 39.27%
## Sequence ID: contig_8    Length: 1385    GC Content: 34.37%
## Sequence ID: contig_18   Length: 2540    GC Content: 34.13%
## Sequence ID: contig_26   Length: 1989    GC Content: 42.23%
## Sequence ID: contig_16   Length: 5025    GC Content: 32.60%
## Sequence ID: contig_21   Length: 2534    GC Content: 37.37%

Flye assembly without option --meta

flye --nano-raw 00_RAW_DATA/Cel_g3_SUP_noCulex.fastq.gz \
     --out-dir 02_ASSEMBLY_onlybac 

grep -F -e "root: INFO:" -e "DEBUG: Cmd:" -e "  Total" -e " Fragments" -e " Mean cov" 02_ASSEMBLY_no_meta/flye.log

## [2026-05-26 17:33:09] root: INFO: Starting Flye 2.9.1-b1780
## [2026-05-26 17:33:09] root: DEBUG: Cmd: /home/mmahout/miniforge3/envs/flye291/bin/flye --nano-raw Cel_g3_SUP_noCulex.fastq.gz --out-dir 02_ASSEMBLY_no_meta
## [2026-05-26 17:33:09] root: INFO: >>>STAGE: configure
## [2026-05-26 17:33:09] root: INFO: Configuring run
## [2026-05-26 17:33:10] root: INFO: Total read length: 63028141
## [2026-05-26 17:33:10] root: INFO: Reads N50/N90: 2979 / 566
## [2026-05-26 17:33:10] root: INFO: Minimum overlap set to 1000
## [2026-05-26 17:33:10] root: INFO: >>>STAGE: assembly
## [2026-05-26 17:33:10] root: INFO: Assembling disjointigs
## [2026-05-26 17:37:33] root: INFO: >>>STAGE: consensus
## [2026-05-26 17:37:33] root: INFO: Running Minimap2
## [2026-05-26 17:38:00] root: INFO: Computing consensus
## [2026-05-26 17:38:25] root: INFO: Alignment error rate: 0.088233
## [2026-05-26 17:38:25] root: INFO: >>>STAGE: repeat
## [2026-05-26 17:38:25] root: INFO: Building and resolving repeat graph
## [2026-05-26 17:38:56] root: INFO: >>>STAGE: contigger
## [2026-05-26 17:38:56] root: INFO: Generating contigs
## [2026-05-26 17:38:57] root: INFO: >>>STAGE: polishing
## [2026-05-26 17:38:57] root: INFO: Polishing genome (1/1)
## [2026-05-26 17:38:57] root: INFO: Running minimap2
## [2026-05-26 17:39:21] root: INFO: Separating alignment into bubbles
## [2026-05-26 17:39:47] root: INFO: Alignment error rate: 0.056615
## [2026-05-26 17:39:47] root: INFO: Correcting bubbles
## [2026-05-26 17:41:28] root: INFO: >>>STAGE: finalize
## [2026-05-26 17:41:28] root: INFO: Assembly statistics:
##  Total length:   1517479
##  Fragments:  27
##  Fragments N50:  1202248
##  Mean coverage:  33
## [2026-05-26 17:41:28] root: INFO: Final assembly: /home/mmahout/Desktop/WORK/CelG/02_ASSEMBLY_no_meta/assembly.fasta

# get non-Wolbachia contig names
comm -23 <(grep ">" 02_ASSEMBLY_no_meta/assembly.fasta | cut -f 2 -d">") <(minimap2 CelG_Assembly/assembly.fasta 02_ASSEMBLY_no_meta/assembly.fasta | grep -v "\[" | cut -f 1 | uniq) >  02_ASSEMBLY_no_meta/contigs_to_remove.txt

## [M::mm_idx_gen::0.041*1.03] collected minimizers
## [M::mm_idx_gen::0.052*1.44] sorted minimizers
## [M::main::0.052*1.43] loaded/built the index for 24 target sequence(s)
## [M::mm_mapopt_update::0.056*1.41] mid_occ = 50
## [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 24
## [M::mm_idx_stat::0.058*1.39] distinct minimizers: 240969 (93.30% are singletons); average occurrences: 1.172; average spacing: 5.367; total length: 1515310
## [M::worker_pipeline::1.951*1.11] mapped 27 sequences
## [M::main] Version: 2.26-r1175
## [M::main] CMD: minimap2 CelG_Assembly/assembly.fasta 02_ASSEMBLY_no_meta/assembly.fasta
## [M::main] Real time: 1.954 sec; CPU: 2.160 sec; Peak RSS: 0.079 GB

cd 02_ASSEMBLY_no_meta/ && cat contigs_to_remove.txt && wc -l contigs_to_remove.txt && cd ..

## contig_31
## contig_32
## contig_34
## contig_35
## 4 contigs_to_remove.txt

cd 02_ASSEMBLY_no_meta/ && cp assembly.fasta assembly.fasta.bak && seqkit grep -v -f contigs_to_remove.txt assembly.fasta.bak -o assembly.fasta && cd ..

## [INFO] 4 patterns loaded from file

cd 02_ASSEMBLY_no_meta/ && grep ">" assembly.fasta -c; echo "(number of contigs)" && cd ..

## 23
## (number of contigs)

cd 02_ASSEMBLY_no_meta/ && /home/mmahout/miniforge3/bin/python sequence_lengths.py && cd ..

## Sequence ID: contig_1    Length: 1202248 GC Content: 34.07%
## Sequence ID: contig_10   Length: 5460    GC Content: 34.03%
## Sequence ID: contig_11   Length: 3752    GC Content: 34.59%
## Sequence ID: contig_12   Length: 3950    GC Content: 34.18%
## Sequence ID: contig_13   Length: 1388    GC Content: 34.44%
## Sequence ID: contig_14   Length: 7854    GC Content: 35.74%
## Sequence ID: contig_16   Length: 1456    GC Content: 30.49%
## Sequence ID: contig_17   Length: 2646    GC Content: 31.56%
## Sequence ID: contig_19   Length: 11695   GC Content: 33.61%
## Sequence ID: contig_2    Length: 39979   GC Content: 34.03%
## Sequence ID: contig_20   Length: 6279    GC Content: 33.78%
## Sequence ID: contig_21   Length: 8206    GC Content: 32.98%
## Sequence ID: contig_24   Length: 1357    GC Content: 34.49%
## Sequence ID: contig_28   Length: 5508    GC Content: 33.33%
## Sequence ID: contig_29   Length: 5023    GC Content: 32.61%
## Sequence ID: contig_30   Length: 1989    GC Content: 42.23%
## Sequence ID: contig_33   Length: 1561    GC Content: 33.57%
## Sequence ID: contig_37   Length: 7855    GC Content: 35.74%
## Sequence ID: contig_4    Length: 1273    GC Content: 32.99%
## Sequence ID: contig_6    Length: 12458   GC Content: 33.48%
## Sequence ID: contig_7    Length: 1335    GC Content: 38.58%
## Sequence ID: contig_8    Length: 135448  GC Content: 34.89%
## Sequence ID: contig_9    Length: 10443   GC Content: 35.29%

Pros: genome seems slightly less fragmented. Cons: no clear assembly of plasmid. Only circular contig is contig_30, plasmid matches partially with contig_14.

Flye assembly with options --nano-hq --read-error .05 and with option --meta

flye --nano-hq 00_RAW_DATA/Cel_g3_SUP_noCulex.fastq.gz --read-error .05 \
     --out-dir 02_ASSEMBLY_hq_005 --meta

grep -F -e "root: INFO:" -e "DEBUG: Cmd:" -e "  Total" -e " Fragments" -e " Mean cov" 02_ASSEMBLY_hq_005/flye.log

## [2026-05-26 16:34:01] root: INFO: Starting Flye 2.9.1-b1780
## [2026-05-26 16:34:01] root: DEBUG: Cmd: /home/mmahout/miniforge3/envs/flye291/bin/flye --read-error .05 --nano-hq Cel_g3_SUP_noCulex.fastq.gz --out-dir 02_ASSEMBLY_hq_005 --meta
## [2026-05-26 16:34:01] root: INFO: >>>STAGE: configure
## [2026-05-26 16:34:01] root: INFO: Configuring run
## [2026-05-26 16:34:02] root: INFO: Total read length: 63028141
## [2026-05-26 16:34:02] root: INFO: Reads N50/N90: 2979 / 566
## [2026-05-26 16:34:02] root: INFO: Minimum overlap set to 1000
## [2026-05-26 16:34:02] root: INFO: >>>STAGE: assembly
## [2026-05-26 16:34:02] root: INFO: Assembling disjointigs
## [2026-05-26 16:35:23] root: INFO: >>>STAGE: consensus
## [2026-05-26 16:35:23] root: INFO: Running Minimap2
## [2026-05-26 16:35:52] root: INFO: Computing consensus
## [2026-05-26 16:36:19] root: INFO: Alignment error rate: 0.084672
## [2026-05-26 16:36:19] root: INFO: >>>STAGE: repeat
## [2026-05-26 16:36:19] root: INFO: Building and resolving repeat graph
## [2026-05-26 16:37:52] root: INFO: >>>STAGE: contigger
## [2026-05-26 16:37:52] root: INFO: Generating contigs
## [2026-05-26 16:37:53] root: INFO: >>>STAGE: polishing
## [2026-05-26 16:37:53] root: INFO: Polishing genome (1/1)
## [2026-05-26 16:37:53] root: INFO: Running minimap2
## [2026-05-26 16:38:17] root: INFO: Separating alignment into bubbles
## [2026-05-26 16:38:44] root: INFO: Alignment error rate: 0.056646
## [2026-05-26 16:38:44] root: INFO: Correcting bubbles
## [2026-05-26 16:39:24] root: INFO: >>>STAGE: finalize
## [2026-05-26 16:39:24] root: INFO: Assembly statistics:
##  Total length:   1620880
##  Fragments:  33
##  Fragments N50:  1196640
##  Mean coverage:  33
## [2026-05-26 16:39:24] root: INFO: Final assembly: /home/mmahout/Desktop/WORK/CelG/02_ASSEMBLY_hq_005/assembly.fasta

# get non-Wolbachia contig names
comm -23 <(grep ">" 02_ASSEMBLY_hq_005/assembly.fasta | cut -f 2 -d">") <(minimap2 CelG_Assembly/assembly.fasta 02_ASSEMBLY_hq_005/assembly.fasta | grep -v "\[" | cut -f 1 | uniq) >  02_ASSEMBLY_hq_005/contigs_to_remove.txt

## [M::mm_idx_gen::0.038*1.04] collected minimizers
## [M::mm_idx_gen::0.048*1.44] sorted minimizers
## [M::main::0.048*1.44] loaded/built the index for 24 target sequence(s)
## [M::mm_mapopt_update::0.052*1.41] mid_occ = 50
## [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 24
## [M::mm_idx_stat::0.055*1.39] distinct minimizers: 240969 (93.30% are singletons); average occurrences: 1.172; average spacing: 5.367; total length: 1515310
## [M::worker_pipeline::1.958*1.16] mapped 33 sequences
## [M::main] Version: 2.26-r1175
## [M::main] CMD: minimap2 CelG_Assembly/assembly.fasta 02_ASSEMBLY_hq_005/assembly.fasta
## [M::main] Real time: 1.963 sec; CPU: 2.272 sec; Peak RSS: 0.079 GB

cd 02_ASSEMBLY_hq_005/ && cat contigs_to_remove.txt && wc -l contigs_to_remove.txt && cd ..

## contig_24
## contig_35
## contig_36
## contig_37
## contig_38
## contig_39
## contig_40
## 7 contigs_to_remove.txt

cd 02_ASSEMBLY_hq_005/ && cp assembly.fasta assembly.fasta.bak && seqkit grep -v -f contigs_to_remove.txt assembly.fasta.bak -o assembly.fasta && cd ..

## [INFO] 7 patterns loaded from file

cd 02_ASSEMBLY_hq_005/ && grep ">" assembly.fasta -c; echo "(number of contigs)" && cd ..

## 26
## (number of contigs)

cd 02_ASSEMBLY_hq_005/ && /home/mmahout/miniforge3/bin/python sequence_lengths.py && cd ..

## Sequence ID: contig_1    Length: 8552    GC Content: 36.74%
## Sequence ID: contig_10   Length: 12621   GC Content: 35.27%
## Sequence ID: contig_11   Length: 7950    GC Content: 33.40%
## Sequence ID: contig_12   Length: 1386    GC Content: 34.42%
## Sequence ID: contig_13   Length: 3305    GC Content: 35.01%
## Sequence ID: contig_14   Length: 1196640 GC Content: 34.08%
## Sequence ID: contig_15   Length: 3734    GC Content: 34.20%
## Sequence ID: contig_16   Length: 3990    GC Content: 34.24%
## Sequence ID: contig_17   Length: 7661    GC Content: 33.23%
## Sequence ID: contig_2    Length: 8220    GC Content: 32.98%
## Sequence ID: contig_21   Length: 7511    GC Content: 36.91%
## Sequence ID: contig_23   Length: 13645   GC Content: 34.56%
## Sequence ID: contig_26   Length: 11564   GC Content: 35.38%
## Sequence ID: contig_27   Length: 39323   GC Content: 33.85%
## Sequence ID: contig_3    Length: 122783  GC Content: 34.73%
## Sequence ID: contig_30   Length: 548 GC Content: 35.58%
## Sequence ID: contig_31   Length: 1381    GC Content: 34.32%
## Sequence ID: contig_32   Length: 5633    GC Content: 35.26%
## Sequence ID: contig_34   Length: 681 GC Content: 37.89%
## Sequence ID: contig_4    Length: 33543   GC Content: 34.43%
## Sequence ID: contig_41   Length: 5042    GC Content: 33.14%
## Sequence ID: contig_42   Length: 18481   GC Content: 35.55%
## Sequence ID: contig_5    Length: 2605    GC Content: 34.17%
## Sequence ID: contig_6    Length: 3586    GC Content: 36.87%
## Sequence ID: contig_7    Length: 5025    GC Content: 32.60%
## Sequence ID: contig_9    Length: 2649    GC Content: 31.52%

Pros: similar assembly of plasmid (contig_42). Cons: genome even more fragmented, two more contigs, including two smaller than 1000 bp instead of one.

Flye assembly with options --nano-hq --read-error .05 and without option --meta

flye --nano-hq 00_RAW_DATA/Cel_g3_SUP_noCulex.fastq.gz --read-error .05 \
     --out-dir 02_ASSEMBLY_hq_005_no_meta 

grep -F -e "root: INFO:" -e "DEBUG: Cmd:" -e "  Total" -e " Fragments" -e " Mean cov" 02_ASSEMBLY_hq_005_no_meta/flye.log

## [2026-05-27 16:10:32] root: INFO: Starting Flye 2.9.1-b1780
## [2026-05-27 16:10:32] root: DEBUG: Cmd: /home/mmahout/miniforge3/envs/flye291/bin/flye --nano-hq Cel_g3_SUP_noCulex.fastq.gz --read-error .05 --out-dir 02_ASSEMBLY_hq_005_no_meta
## [2026-05-27 16:10:32] root: INFO: >>>STAGE: configure
## [2026-05-27 16:10:32] root: INFO: Configuring run
## [2026-05-27 16:10:33] root: INFO: Total read length: 63028141
## [2026-05-27 16:10:33] root: INFO: Reads N50/N90: 2979 / 566
## [2026-05-27 16:10:33] root: INFO: Minimum overlap set to 1000
## [2026-05-27 16:10:33] root: INFO: >>>STAGE: assembly
## [2026-05-27 16:10:33] root: INFO: Assembling disjointigs
## [2026-05-27 16:11:51] root: INFO: >>>STAGE: consensus
## [2026-05-27 16:11:51] root: INFO: Running Minimap2
## [2026-05-27 16:12:21] root: INFO: Computing consensus
## [2026-05-27 16:12:47] root: INFO: Alignment error rate: 0.084218
## [2026-05-27 16:12:47] root: INFO: >>>STAGE: repeat
## [2026-05-27 16:12:47] root: INFO: Building and resolving repeat graph
## [2026-05-27 16:13:07] root: INFO: >>>STAGE: contigger
## [2026-05-27 16:13:07] root: INFO: Generating contigs
## [2026-05-27 16:13:08] root: INFO: >>>STAGE: polishing
## [2026-05-27 16:13:08] root: INFO: Polishing genome (1/1)
## [2026-05-27 16:13:08] root: INFO: Running minimap2
## [2026-05-27 16:13:34] root: INFO: Separating alignment into bubbles
## [2026-05-27 16:14:01] root: INFO: Alignment error rate: 0.055687
## [2026-05-27 16:14:01] root: INFO: Correcting bubbles
## [2026-05-27 16:14:43] root: INFO: >>>STAGE: finalize
## [2026-05-27 16:14:43] root: INFO: Assembly statistics:
##  Total length:   1559659
##  Fragments:  28
##  Fragments N50:  1201018
##  Mean coverage:  33
## [2026-05-27 16:14:43] root: INFO: Final assembly: /home/mmahout/Desktop/WORK/CelG/02_ASSEMBLY_hq_005_no_meta/assembly.fasta

# get non-Wolbachia contig names
comm -23 <(grep ">" 02_ASSEMBLY_hq_005_no_meta/assembly.fasta | cut -f 2 -d">") <(minimap2 CelG_Assembly/assembly.fasta 02_ASSEMBLY_hq_005_no_meta/assembly.fasta | grep -v "\[" | cut -f 1 | uniq) >  02_ASSEMBLY_hq_005_no_meta/contigs_to_remove.txt

## [M::mm_idx_gen::0.043*1.03] collected minimizers
## [M::mm_idx_gen::0.055*1.42] sorted minimizers
## [M::main::0.055*1.42] loaded/built the index for 24 target sequence(s)
## [M::mm_mapopt_update::0.058*1.39] mid_occ = 50
## [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 24
## [M::mm_idx_stat::0.061*1.38] distinct minimizers: 240969 (93.30% are singletons); average occurrences: 1.172; average spacing: 5.367; total length: 1515310
## [M::worker_pipeline::1.922*1.13] mapped 28 sequences
## [M::main] Version: 2.26-r1175
## [M::main] CMD: minimap2 CelG_Assembly/assembly.fasta 02_ASSEMBLY_hq_005_no_meta/assembly.fasta
## [M::main] Real time: 1.927 sec; CPU: 2.174 sec; Peak RSS: 0.080 GB

cd 02_ASSEMBLY_hq_005_no_meta/ && cat contigs_to_remove.txt && wc -l contigs_to_remove.txt && cd ..

## contig_35
## contig_36
## contig_37
## contig_38
## 4 contigs_to_remove.txt

cd 02_ASSEMBLY_hq_005_no_meta/ && cp assembly.fasta assembly.fasta.bak && seqkit grep -v -f contigs_to_remove.txt assembly.fasta.bak -o assembly.fasta && cd ..

## [INFO] 4 patterns loaded from file

cd 02_ASSEMBLY_hq_005_no_meta/ && grep ">" assembly.fasta -c; echo "(number of contigs)" && cd ..

## 24
## (number of contigs)

cd 02_ASSEMBLY_hq_005_no_meta/ && /home/mmahout/miniforge3/bin/python sequence_lengths.py && cd ..

## Sequence ID: contig_11   Length: 7856    GC Content: 35.74%
## Sequence ID: contig_13   Length: 1201018 GC Content: 34.07%
## Sequence ID: contig_14   Length: 9660    GC Content: 36.80%
## Sequence ID: contig_15   Length: 3734    GC Content: 34.20%
## Sequence ID: contig_16   Length: 3991    GC Content: 34.23%
## Sequence ID: contig_17   Length: 11077   GC Content: 35.03%
## Sequence ID: contig_18   Length: 11767   GC Content: 33.81%
## Sequence ID: contig_19   Length: 4675    GC Content: 33.97%
## Sequence ID: contig_2    Length: 8220    GC Content: 32.98%
## Sequence ID: contig_22   Length: 1831    GC Content: 32.61%
## Sequence ID: contig_23   Length: 1985    GC Content: 42.22%
## Sequence ID: contig_24   Length: 2553    GC Content: 32.59%
## Sequence ID: contig_26   Length: 9341    GC Content: 34.81%
## Sequence ID: contig_27   Length: 51159   GC Content: 34.33%
## Sequence ID: contig_28   Length: 663 GC Content: 38.91%
## Sequence ID: contig_29   Length: 1676    GC Content: 36.04%
## Sequence ID: contig_3    Length: 135686  GC Content: 34.88%
## Sequence ID: contig_32   Length: 1381    GC Content: 34.32%
## Sequence ID: contig_39   Length: 5041    GC Content: 33.13%
## Sequence ID: contig_4    Length: 11668   GC Content: 33.63%
## Sequence ID: contig_40   Length: 7854    GC Content: 35.74%
## Sequence ID: contig_5    Length: 5025    GC Content: 32.60%
## Sequence ID: contig_7    Length: 2649    GC Content: 31.52%
## Sequence ID: contig_9    Length: 20105   GC Content: 35.33%

Pros: similar genome, contig of ~51 kb. Cons: no clear assembly of plasmid. Only circular contig is contig_23, plasmid matches partially with contig_40.

Flye assembly with reads over 2,000 bp, options --nano-raw, options --keep-haplotypes and --meta

For these four next sections, we created a new file subsampling our reads of with those longer (strictly) than 2,000 bp, using seqtk.

seqtk seq -L 2001 Cel_g3_SUP_noCulex.fastq.gz | gzip > Cel_g3_SUP_noCulex.2000bp.fastq.gz

flye --nano-raw 00_RAW_DATA/Cel_g3_SUP_noCulex.2000bp.fastq.gz \
     --out-dir 02_ASSEMBLY_meta_2000bp_haplotypes --meta --keep-haplotypes

grep -F -e "root: INFO:" -e "DEBUG: Cmd:" -e "  Total" -e " Fragments" -e " Mean cov" 02_ASSEMBLY_meta_2000bp_haplotypes/flye.log

## [2026-05-26 17:21:14] root: INFO: Starting Flye 2.9.1-b1780
## [2026-05-26 17:21:14] root: DEBUG: Cmd: /home/mmahout/miniforge3/envs/flye291/bin/flye --nano-raw Cel_g3_SUP_noCulex.2000bp.fastq.gz --meta --out-dir 02_ASSEMBLY_meta_2000bp_haplotypes --meta --keep-haplotypes
## [2026-05-26 17:21:14] root: INFO: >>>STAGE: configure
## [2026-05-26 17:21:14] root: INFO: Configuring run
## [2026-05-26 17:21:14] root: INFO: Total read length: 39823146
## [2026-05-26 17:21:14] root: INFO: Reads N50/N90: 5701 / 2406
## [2026-05-26 17:21:14] root: INFO: Minimum overlap set to 2000
## [2026-05-26 17:21:14] root: INFO: >>>STAGE: assembly
## [2026-05-26 17:21:14] root: INFO: Assembling disjointigs
## [2026-05-26 17:25:23] root: INFO: >>>STAGE: consensus
## [2026-05-26 17:25:23] root: INFO: Running Minimap2
## [2026-05-26 17:25:42] root: INFO: Computing consensus
## [2026-05-26 17:26:02] root: INFO: Alignment error rate: 0.094121
## [2026-05-26 17:26:02] root: INFO: >>>STAGE: repeat
## [2026-05-26 17:26:02] root: INFO: Building and resolving repeat graph
## [2026-05-26 17:26:39] root: INFO: >>>STAGE: contigger
## [2026-05-26 17:26:39] root: INFO: Generating contigs
## [2026-05-26 17:26:39] root: INFO: >>>STAGE: polishing
## [2026-05-26 17:26:39] root: INFO: Polishing genome (1/1)
## [2026-05-26 17:26:39] root: INFO: Running minimap2
## [2026-05-26 17:26:55] root: INFO: Separating alignment into bubbles
## [2026-05-26 17:27:16] root: INFO: Alignment error rate: 0.057080
## [2026-05-26 17:27:16] root: INFO: Correcting bubbles
## [2026-05-26 17:28:27] root: INFO: >>>STAGE: finalize
## [2026-05-26 17:28:27] root: INFO: Assembly statistics:
##  Total length:   1572029
##  Fragments:  17
##  Fragments N50:  1185389
##  Mean coverage:  23
## [2026-05-26 17:28:27] root: INFO: Final assembly: /home/mmahout/Desktop/WORK/CelG/02_ASSEMBLY_meta_2000bp_haplotypes/assembly.fasta

# get non-Wolbachia contig names
comm -23 <(grep ">" 02_ASSEMBLY_meta_2000bp_haplotypes/assembly.fasta | cut -f 2 -d">") <(minimap2 CelG_Assembly/assembly.fasta 02_ASSEMBLY_meta_2000bp_haplotypes/assembly.fasta | grep -v "\[" | cut -f 1 | uniq) >  02_ASSEMBLY_meta_2000bp_haplotypes/contigs_to_remove.txt

## [M::mm_idx_gen::0.033*1.05] collected minimizers
## [M::mm_idx_gen::0.043*1.48] sorted minimizers
## [M::main::0.043*1.48] loaded/built the index for 24 target sequence(s)
## [M::mm_mapopt_update::0.048*1.44] mid_occ = 50
## [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 24
## [M::mm_idx_stat::0.051*1.41] distinct minimizers: 240969 (93.30% are singletons); average occurrences: 1.172; average spacing: 5.367; total length: 1515310
## [M::worker_pipeline::1.904*1.15] mapped 17 sequences
## [M::main] Version: 2.26-r1175
## [M::main] CMD: minimap2 CelG_Assembly/assembly.fasta 02_ASSEMBLY_meta_2000bp_haplotypes/assembly.fasta
## [M::main] Real time: 1.910 sec; CPU: 2.187 sec; Peak RSS: 0.081 GB

cd 02_ASSEMBLY_meta_2000bp_haplotypes/ && cat contigs_to_remove.txt && wc -l contigs_to_remove.txt && cd ..

## contig_15
## contig_16
## contig_18
## contig_19
## 4 contigs_to_remove.txt

cd 02_ASSEMBLY_meta_2000bp_haplotypes/ && cp assembly.fasta assembly.fasta.bak && seqkit grep -v -f contigs_to_remove.txt assembly.fasta.bak -o assembly.fasta && cd ..

## [INFO] 4 patterns loaded from file

cd 02_ASSEMBLY_meta_2000bp_haplotypes/ && grep ">" assembly.fasta -c; echo "(number of contigs)" && cd ..

## 13
## (number of contigs)

cd 02_ASSEMBLY_meta_2000bp_haplotypes/ && /home/mmahout/miniforge3/bin/python sequence_lengths.py && cd ..

## Sequence ID: contig_1    Length: 141234  GC Content: 34.73%
## Sequence ID: contig_10   Length: 2183    GC Content: 33.76%
## Sequence ID: contig_11   Length: 9819    GC Content: 34.14%
## Sequence ID: contig_12   Length: 2646    GC Content: 31.56%
## Sequence ID: contig_13   Length: 9856    GC Content: 35.26%
## Sequence ID: contig_2    Length: 11487   GC Content: 34.20%
## Sequence ID: contig_23   Length: 18484   GC Content: 35.54%
## Sequence ID: contig_3    Length: 1185389 GC Content: 34.08%
## Sequence ID: contig_4    Length: 6874    GC Content: 36.31%
## Sequence ID: contig_5    Length: 74348   GC Content: 35.01%
## Sequence ID: contig_7    Length: 32140   GC Content: 33.65%
## Sequence ID: contig_8    Length: 5508    GC Content: 33.33%
## Sequence ID: contig_9    Length: 5025    GC Content: 32.60%

Flye assembly with reads over 2,000 bp, options --nano-raw, option --keep-haplotypes but without option --meta

flye --nano-raw 00_RAW_DATA/Cel_g3_SUP_noCulex.2000bp.fastq.gz --read-error .05 \
     --out-dir 02_ASSEMBLY_no_meta_2000bp_haplotypes --keep-haplotypes

grep -F -e "root: INFO:" -e "DEBUG: Cmd:" -e "  Total" -e " Fragments" -e " Mean cov" 02_ASSEMBLY_no_meta_2000bp_haplotypes/flye.log

## [2026-05-28 09:46:11] root: INFO: Starting Flye 2.9.1-b1780
## [2026-05-28 09:46:11] root: DEBUG: Cmd: /home/mmahout/miniforge3/envs/flye291/bin/flye --nano-raw Cel_g3_SUP_noCulex.2000bp.fastq.gz --out-dir 02_ASSEMBLY_no_meta_2000bp_haplotypes --keep-haplotypes
## [2026-05-28 09:46:11] root: INFO: >>>STAGE: configure
## [2026-05-28 09:46:11] root: INFO: Configuring run
## [2026-05-28 09:46:11] root: INFO: Total read length: 39823146
## [2026-05-28 09:46:11] root: INFO: Reads N50/N90: 5701 / 2406
## [2026-05-28 09:46:11] root: INFO: Minimum overlap set to 2000
## [2026-05-28 09:46:11] root: INFO: >>>STAGE: assembly
## [2026-05-28 09:46:11] root: INFO: Assembling disjointigs
## [2026-05-28 09:50:09] root: INFO: >>>STAGE: consensus
## [2026-05-28 09:50:09] root: INFO: Running Minimap2
## [2026-05-28 09:50:27] root: INFO: Computing consensus
## [2026-05-28 09:50:45] root: INFO: Alignment error rate: 0.094167
## [2026-05-28 09:50:45] root: INFO: >>>STAGE: repeat
## [2026-05-28 09:50:45] root: INFO: Building and resolving repeat graph
## [2026-05-28 09:51:12] root: INFO: >>>STAGE: contigger
## [2026-05-28 09:51:12] root: INFO: Generating contigs
## [2026-05-28 09:51:13] root: INFO: >>>STAGE: polishing
## [2026-05-28 09:51:13] root: INFO: Polishing genome (1/1)
## [2026-05-28 09:51:13] root: INFO: Running minimap2
## [2026-05-28 09:51:28] root: INFO: Separating alignment into bubbles
## [2026-05-28 09:51:47] root: INFO: Alignment error rate: 0.057414
## [2026-05-28 09:51:47] root: INFO: Correcting bubbles
## [2026-05-28 09:52:24] root: INFO: >>>STAGE: finalize
## [2026-05-28 09:52:24] root: INFO: Assembly statistics:
##  Total length:   1527164
##  Fragments:  23
##  Fragments N50:  1202901
##  Mean coverage:  23
## [2026-05-28 09:52:24] root: INFO: Final assembly: /home/mmahout/Desktop/WORK/CelG/02_ASSEMBLY_no_meta_2000bp_haplotypes/assembly.fasta

# get non-Wolbachia contig names
comm -23 <(grep ">" 02_ASSEMBLY_no_meta_2000bp_haplotypes/assembly.fasta | cut -f 2 -d">") <(minimap2 CelG_Assembly/assembly.fasta 02_ASSEMBLY_no_meta_2000bp_haplotypes/assembly.fasta | grep -v "\[" | cut -f 1 | uniq) >  02_ASSEMBLY_no_meta_2000bp_haplotypes/contigs_to_remove.txt

## [M::mm_idx_gen::0.040*1.04] collected minimizers
## [M::mm_idx_gen::0.050*1.42] sorted minimizers
## [M::main::0.050*1.42] loaded/built the index for 24 target sequence(s)
## [M::mm_mapopt_update::0.055*1.38] mid_occ = 50
## [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 24
## [M::mm_idx_stat::0.058*1.36] distinct minimizers: 240969 (93.30% are singletons); average occurrences: 1.172; average spacing: 5.367; total length: 1515310
## [M::worker_pipeline::1.968*1.09] mapped 23 sequences
## [M::main] Version: 2.26-r1175
## [M::main] CMD: minimap2 CelG_Assembly/assembly.fasta 02_ASSEMBLY_no_meta_2000bp_haplotypes/assembly.fasta
## [M::main] Real time: 1.974 sec; CPU: 2.145 sec; Peak RSS: 0.078 GB

cd 02_ASSEMBLY_no_meta_2000bp_haplotypes/ && cat contigs_to_remove.txt && wc -l contigs_to_remove.txt && cd ..

## contig_25
## contig_26
## 2 contigs_to_remove.txt

cd 02_ASSEMBLY_no_meta_2000bp_haplotypes/ && cp assembly.fasta assembly.fasta.bak && seqkit grep -v -f contigs_to_remove.txt assembly.fasta.bak -o assembly.fasta && cd ..

## [INFO] 2 patterns loaded from file

cd 02_ASSEMBLY_no_meta_2000bp_haplotypes/ && grep ">" assembly.fasta -c; echo "(number of contigs)" && cd ..

## 21
## (number of contigs)

cd 02_ASSEMBLY_no_meta_2000bp_haplotypes/ && /home/mmahout/miniforge3/bin/python sequence_lengths.py && cd ..

## Sequence ID: contig_1    Length: 45545   GC Content: 34.83%
## Sequence ID: contig_10   Length: 543 GC Content: 31.12%
## Sequence ID: contig_11   Length: 14649   GC Content: 34.02%
## Sequence ID: contig_12   Length: 5508    GC Content: 33.33%
## Sequence ID: contig_13   Length: 5025    GC Content: 32.60%
## Sequence ID: contig_14   Length: 2183    GC Content: 33.67%
## Sequence ID: contig_16   Length: 2646    GC Content: 31.56%
## Sequence ID: contig_18   Length: 4679    GC Content: 33.38%
## Sequence ID: contig_2    Length: 75606   GC Content: 34.89%
## Sequence ID: contig_22   Length: 14713   GC Content: 33.94%
## Sequence ID: contig_23   Length: 3230    GC Content: 32.72%
## Sequence ID: contig_29   Length: 5777    GC Content: 36.87%
## Sequence ID: contig_3    Length: 8830    GC Content: 33.94%
## Sequence ID: contig_30   Length: 10344   GC Content: 33.60%
## Sequence ID: contig_31   Length: 7758    GC Content: 33.76%
## Sequence ID: contig_34   Length: 18484   GC Content: 35.54%
## Sequence ID: contig_4    Length: 1202901 GC Content: 34.07%
## Sequence ID: contig_5    Length: 554 GC Content: 35.56%
## Sequence ID: contig_6    Length: 1581    GC Content: 34.22%
## Sequence ID: contig_7    Length: 14809   GC Content: 33.40%
## Sequence ID: contig_9    Length: 46402   GC Content: 34.33%

Flye assembly with reads over 2,000 bp, options --nano-hq --read-error .05, options --keep-haplotypes and --meta

flye --nano-hq 00_RAW_DATA/Cel_g3_SUP_noCulex.2000bp.fastq.gz --read-error .05 \
     --out-dir 02_ASSEMBLY_hq_005_meta_2000_bp_keep_haplotypes --meta --keep-haplotypes

grep -F -e "root: INFO:" -e "DEBUG: Cmd:" -e "  Total" -e " Fragments" -e " Mean cov" 02_ASSEMBLY_hq_005_meta_2000_bp_keep_haplotypes/flye.log

## [2026-05-26 16:06:02] root: INFO: Starting Flye 2.9.1-b1780
## [2026-05-26 16:06:02] root: DEBUG: Cmd: /home/mmahout/miniforge3/envs/flye291/bin/flye --read-error .05 --keep-haplotypes --nano-hq Cel_g3_SUP_noCulex.2000bp.fastq.gz --meta --out-dir 02_ASSEMBLY_hq_005_meta_2000_bp_keep_haplotypes
## [2026-05-26 16:06:02] root: INFO: >>>STAGE: configure
## [2026-05-26 16:06:02] root: INFO: Configuring run
## [2026-05-26 16:06:02] root: INFO: Total read length: 39823146
## [2026-05-26 16:06:02] root: INFO: Reads N50/N90: 5701 / 2406
## [2026-05-26 16:06:02] root: INFO: Minimum overlap set to 2000
## [2026-05-26 16:06:02] root: INFO: >>>STAGE: assembly
## [2026-05-26 16:06:02] root: INFO: Assembling disjointigs
## [2026-05-26 16:07:53] root: INFO: >>>STAGE: consensus
## [2026-05-26 16:07:53] root: INFO: Running Minimap2
## [2026-05-26 16:08:11] root: INFO: Computing consensus
## [2026-05-26 16:08:43] root: INFO: Alignment error rate: 0.090406
## [2026-05-26 16:08:43] root: INFO: >>>STAGE: repeat
## [2026-05-26 16:08:43] root: INFO: Building and resolving repeat graph
## [2026-05-26 16:09:09] root: INFO: >>>STAGE: contigger
## [2026-05-26 16:09:09] root: INFO: Generating contigs
## [2026-05-26 16:09:10] root: INFO: >>>STAGE: polishing
## [2026-05-26 16:09:10] root: INFO: Polishing genome (1/1)
## [2026-05-26 16:09:10] root: INFO: Running minimap2
## [2026-05-26 16:09:25] root: INFO: Separating alignment into bubbles
## [2026-05-26 16:09:45] root: INFO: Alignment error rate: 0.055993
## [2026-05-26 16:09:45] root: INFO: Correcting bubbles
## [2026-05-26 16:10:34] root: INFO: >>>STAGE: finalize
## [2026-05-26 16:10:34] root: INFO: Assembly statistics:
##  Total length:   1588419
##  Fragments:  25
##  Fragments N50:  1202866
##  Mean coverage:  22
## [2026-05-26 16:10:34] root: INFO: Final assembly: /home/mmahout/Desktop/WORK/CelG/02_ASSEMBLY_hq_005_meta_2000_bp_keep_haplotypes/assembly.fasta

# get non-Wolbachia contig names
comm -23 <(grep ">" 02_ASSEMBLY_hq_005_meta_2000_bp_keep_haplotypes/assembly.fasta | cut -f 2 -d">") <(minimap2 CelG_Assembly/assembly.fasta 02_ASSEMBLY_hq_005_meta_2000_bp_keep_haplotypes/assembly.fasta | grep -v "\[" | cut -f 1 | uniq) >  02_ASSEMBLY_hq_005_meta_2000_bp_keep_haplotypes/contigs_to_remove.txt

## [M::mm_idx_gen::0.034*1.05] collected minimizers
## [M::mm_idx_gen::0.044*1.47] sorted minimizers
## [M::main::0.044*1.47] loaded/built the index for 24 target sequence(s)
## [M::mm_mapopt_update::0.048*1.43] mid_occ = 50
## [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 24
## [M::mm_idx_stat::0.050*1.41] distinct minimizers: 240969 (93.30% are singletons); average occurrences: 1.172; average spacing: 5.367; total length: 1515310
## [M::worker_pipeline::1.912*1.14] mapped 25 sequences
## [M::main] Version: 2.26-r1175
## [M::main] CMD: minimap2 CelG_Assembly/assembly.fasta 02_ASSEMBLY_hq_005_meta_2000_bp_keep_haplotypes/assembly.fasta
## [M::main] Real time: 1.916 sec; CPU: 2.185 sec; Peak RSS: 0.079 GB

cd 02_ASSEMBLY_hq_005_meta_2000_bp_keep_haplotypes/ && cat contigs_to_remove.txt && wc -l contigs_to_remove.txt && cd ..

## contig_21
## contig_22
## contig_23
## contig_24
## contig_25
## 5 contigs_to_remove.txt

cd 02_ASSEMBLY_hq_005_meta_2000_bp_keep_haplotypes/ && cp assembly.fasta assembly.fasta.bak && seqkit grep -v -f contigs_to_remove.txt assembly.fasta.bak -o assembly.fasta && cd ..

## [INFO] 5 patterns loaded from file

cd 02_ASSEMBLY_hq_005_meta_2000_bp_keep_haplotypes/ && grep ">" assembly.fasta -c; echo "(number of contigs)" && cd ..

## 20
## (number of contigs)

cd 02_ASSEMBLY_hq_005_meta_2000_bp_keep_haplotypes/ && /home/mmahout/miniforge3/bin/python sequence_lengths.py && cd ..

## Sequence ID: contig_1    Length: 540 GC Content: 31.30%
## Sequence ID: contig_10   Length: 10457   GC Content: 34.07%
## Sequence ID: contig_11   Length: 1202866 GC Content: 34.09%
## Sequence ID: contig_12   Length: 1990    GC Content: 42.26%
## Sequence ID: contig_14   Length: 15395   GC Content: 35.39%
## Sequence ID: contig_15   Length: 42311   GC Content: 33.87%
## Sequence ID: contig_17   Length: 103278  GC Content: 34.62%
## Sequence ID: contig_19   Length: 24538   GC Content: 34.71%
## Sequence ID: contig_2    Length: 5041    GC Content: 33.13%
## Sequence ID: contig_20   Length: 2531    GC Content: 36.86%
## Sequence ID: contig_26   Length: 5777    GC Content: 36.85%
## Sequence ID: contig_27   Length: 14650   GC Content: 34.02%
## Sequence ID: contig_3    Length: 5027    GC Content: 32.58%
## Sequence ID: contig_31   Length: 18480   GC Content: 35.54%
## Sequence ID: contig_4    Length: 2656    GC Content: 34.07%
## Sequence ID: contig_5    Length: 2259    GC Content: 36.52%
## Sequence ID: contig_6    Length: 13446   GC Content: 34.72%
## Sequence ID: contig_7    Length: 2649    GC Content: 31.52%
## Sequence ID: contig_8    Length: 1573    GC Content: 36.68%
## Sequence ID: contig_9    Length: 39975   GC Content: 35.01%

Flye assembly with reads over 2,000 bp, options --nano-hq --read-error .05, option --keep-haplotypes but without option --meta

flye --nano-hq 00_RAW_DATA/Cel_g3_SUP_noCulex.2000bp.fastq.gz --read-error .05 \
     --out-dir 02_ASSEMBLY_hq_005_no_meta_2000_bp_keep_haplotypes --keep-haplotypes

grep -F -e "root: INFO:" -e "DEBUG: Cmd:" -e "  Total" -e " Fragments" -e " Mean cov" 02_ASSEMBLY_hq_005_no_meta_2000_bp_keep_haplotypes/flye.log

## [2026-05-26 16:05:51] root: INFO: Starting Flye 2.9.1-b1780
## [2026-05-26 16:05:51] root: DEBUG: Cmd: /home/mmahout/miniforge3/envs/flye291/bin/flye --read-error .05 --keep-haplotypes --nano-hq Cel_g3_SUP_noCulex.2000bp.fastq.gz --out-dir 02_ASSEMBLY_hq_005_no_meta_2000_bp_keep_haplotypes
## [2026-05-26 16:05:51] root: INFO: >>>STAGE: configure
## [2026-05-26 16:05:51] root: INFO: Configuring run
## [2026-05-26 16:05:52] root: INFO: Total read length: 39823146
## [2026-05-26 16:05:52] root: INFO: Reads N50/N90: 5701 / 2406
## [2026-05-26 16:05:52] root: INFO: Minimum overlap set to 2000
## [2026-05-26 16:05:52] root: INFO: >>>STAGE: assembly
## [2026-05-26 16:05:52] root: INFO: Assembling disjointigs
## [2026-05-26 16:07:29] root: INFO: >>>STAGE: consensus
## [2026-05-26 16:07:29] root: INFO: Running Minimap2
## [2026-05-26 16:07:53] root: INFO: Computing consensus
## [2026-05-26 16:08:13] root: INFO: Alignment error rate: 0.090321
## [2026-05-26 16:08:13] root: INFO: >>>STAGE: repeat
## [2026-05-26 16:08:13] root: INFO: Building and resolving repeat graph
## [2026-05-26 16:08:36] root: INFO: >>>STAGE: contigger
## [2026-05-26 16:08:36] root: INFO: Generating contigs
## [2026-05-26 16:08:37] root: INFO: >>>STAGE: polishing
## [2026-05-26 16:08:37] root: INFO: Polishing genome (1/1)
## [2026-05-26 16:08:37] root: INFO: Running minimap2
## [2026-05-26 16:08:53] root: INFO: Separating alignment into bubbles
## [2026-05-26 16:09:14] root: INFO: Alignment error rate: 0.058221
## [2026-05-26 16:09:14] root: INFO: Correcting bubbles
## [2026-05-26 16:09:45] root: INFO: >>>STAGE: finalize
## [2026-05-26 16:09:45] root: INFO: Assembly statistics:
##  Total length:   1559463
##  Fragments:  14
##  Fragments N50:  1196831
##  Mean coverage:  23
## [2026-05-26 16:09:45] root: INFO: Final assembly: /home/mmahout/Desktop/WORK/CelG/02_ASSEMBLY_hq_005_no_meta_2000_bp_keep_haplotypes/assembly.fasta

# get non-Wolbachia contig names
comm -23 <(grep ">" 02_ASSEMBLY_hq_005_no_meta_2000_bp_keep_haplotypes/assembly.fasta | cut -f 2 -d">") <(minimap2 CelG_Assembly/assembly.fasta 02_ASSEMBLY_hq_005_no_meta_2000_bp_keep_haplotypes/assembly.fasta | grep -v "\[" | cut -f 1 | uniq) >  02_ASSEMBLY_hq_005_no_meta_2000_bp_keep_haplotypes/contigs_to_remove.txt

## [M::mm_idx_gen::0.041*1.05] collected minimizers
## [M::mm_idx_gen::0.051*1.41] sorted minimizers
## [M::main::0.051*1.41] loaded/built the index for 24 target sequence(s)
## [M::mm_mapopt_update::0.055*1.37] mid_occ = 50
## [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 24
## [M::mm_idx_stat::0.058*1.36] distinct minimizers: 240969 (93.30% are singletons); average occurrences: 1.172; average spacing: 5.367; total length: 1515310
## [M::worker_pipeline::1.946*1.12] mapped 14 sequences
## [M::main] Version: 2.26-r1175
## [M::main] CMD: minimap2 CelG_Assembly/assembly.fasta 02_ASSEMBLY_hq_005_no_meta_2000_bp_keep_haplotypes/assembly.fasta
## [M::main] Real time: 1.949 sec; CPU: 2.182 sec; Peak RSS: 0.080 GB

cd 02_ASSEMBLY_hq_005_no_meta_2000_bp_keep_haplotypes/ && cat contigs_to_remove.txt && wc -l contigs_to_remove.txt && cd ..

## contig_20
## contig_21
## 2 contigs_to_remove.txt

cd 02_ASSEMBLY_hq_005_no_meta_2000_bp_keep_haplotypes/ && cp assembly.fasta assembly.fasta.bak && seqkit grep -v -f contigs_to_remove.txt assembly.fasta.bak -o assembly.fasta && cd ..

## [INFO] 2 patterns loaded from file

cd 02_ASSEMBLY_hq_005_no_meta_2000_bp_keep_haplotypes/ && grep ">" assembly.fasta -c; echo "(number of contigs)" && cd ..

## 12
## (number of contigs)

cd 02_ASSEMBLY_hq_005_no_meta_2000_bp_keep_haplotypes/ && /home/mmahout/miniforge3/bin/python sequence_lengths.py && cd ..

## Sequence ID: contig_11   Length: 12965   GC Content: 33.68%
## Sequence ID: contig_12   Length: 1196831 GC Content: 34.08%
## Sequence ID: contig_14   Length: 1990    GC Content: 42.26%
## Sequence ID: contig_16   Length: 51156   GC Content: 34.33%
## Sequence ID: contig_18   Length: 57496   GC Content: 34.97%
## Sequence ID: contig_2    Length: 5042    GC Content: 33.12%
## Sequence ID: contig_26   Length: 18484   GC Content: 35.54%
## Sequence ID: contig_3    Length: 5027    GC Content: 32.58%
## Sequence ID: contig_4    Length: 2660    GC Content: 34.06%
## Sequence ID: contig_6    Length: 136758  GC Content: 34.88%
## Sequence ID: contig_7    Length: 2649    GC Content: 31.52%
## Sequence ID: contig_9    Length: 33800   GC Content: 34.74%

Summary table

  Nb contigs Wolbachia Nb contigs (w/ non-Wolbachia) Circular plasmid assembled (ID, length) Length of longest contig (ID)
flye --meta and --nano-raw (ours) 24 32 (w/ 8) Yes, dimeric (contig_9, 18,485) 1,186,930 (contig_2)
flye --nano-raw 23 27 (w/ 4) No 1,202,248 (contig_1)
flye --nano-hq --read-error .05 --meta 26 33 (w/ 7) Yes, dimeric (contig_42, 18,481) 1,196,640 (contig_14)
flye --nano-hq --read-error .05 24 28 (w/ 4) No 1,201,018 (contig_13)
flye (>2kb) --keep-haplotypes --meta and --nano-raw 13 17 (w/ 4) Yes, dimeric (contig_23, 18,484) 1,185,389 (contig_3)
flye (>2kb) --keep-haplotypes and --nano-raw 21 23 (w/ 2) Yes, dimeric (contig_34, 18,484) 1,202,901 (contig_4)
flye (>2kb) --keep-haplotypes --meta and --nano-hq --read-error .05 20 25 (w/ 5) Yes, dimeric (contig_31, 18,480) 1,202,866 (contig_11)
flye (>2kb) --keep-haplotypes and --nano-hq --read-error .05 12 14 (w/ 2) Yes, dimeric (contig_26, 18,484) 1,196,831 (contig_12)