RosaBioinfo

Bioinformatic analyses and reproducible workflows of ERC RosaLind

In this repository you will find the bioinformatic workflows and analyses conducted as part of the RosaLind ERC.

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Dissection of mosquito ovaries, midgut and salivary glands for microbiome analyses at the organ level

Reproducible bioinformatic analyses for JOVE submission by Tutagata et al.:

• markdown available here
• archive of additional config files here

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Extensive mobilome dynamics in a widespread endosymbiont

Reproducible bioinformatic analyses for Wolbachia mobilome dynamics submitted by Brunner et al.:

• Supplementary Notebook 1: Computational pipeline for treatment of long reads, including masking host reads and assembly of a Wolbachia genome.
• Supplementary Notebook 2: Comparison of flye assemblies with different parameters.
• Supplementary Notebook 3: Estimation of phage region copy number based on the pangenome.
• Supplementary Notebook 4: Extraction and alignment of reads on all contigs before and after filtering, with coverage profiling.
• Supplementary Notebook 5: Mapping plasmid reads over 9,000 nt to the dimeric assembly and reference to evaluate alignment accuracy.
• Supplementary Notebook 6: Extraction of reads >9,000 nt aligning to the plasmid and verification of adapter removal.

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Phage genes promote the pandemic success of a bacterial symbiont

• Supplementary Notebook 1: Quantitative analysis of WO phage induction assays
• Supplementary Notebook 2: Assembly of Isolate and wPipSLAB from short paired-end reads and related analyzes: taxonomical binning and read alignments
• Supplementary Notebook 3: Anvi’o pangenomic analyzes using pWCP, WO, wPipSLAB and wPipPel including addition of metagenomic data layers
• Supplementary Notebook 4: Coverage calculation at gene cluster-level for alignment of Isolate reads and SLAB reads on wPipSLAB
• Supplementary Notebook 5: Coverage visualization of alignment of Isolate reads on wPipPel and WO regions
• Supplementary Notebook 6: Coverage barplot for alignment of Isolate reads on wPipPel regions (WO phage, MLST) and pWCP plasmid
• Supplementary Notebook 7: Coverage visualization of alignment of Isolate reads on Isolate assembly

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Plasmid pWCP is a transcriptionally active component of the Wolbachia mobilome

• Supplementary Notebook 1: RNASeq pipeline of alignment of Culex metatranscriptomic reads to wPipPel and pWCP plasmid with AliNe
• Supplementary Notebook 2: Inter-group and intra-group statistics of expression of pWCP genes in Wolbachia endosymbiont of Culex using RNASeq TPM metric
• Supplementary Notebook 3: RNASeq coverage profiles of pWCP plasmid expression in Wolbachia endosymbiont of Culex
• Supplementary Notebook 4: Inter-stage statistics of expression of pWCP genes in Wolbachia endosymbiont of Culex using RT-qPCR concentrations
• Supplementary Notebook 5: Intra-stage statistics of expression of pWCP genes in Wolbachia endosymbiont of Culex using RT-qPCR concentrations