The Bioinformatics Learning Lab (BILL) is a teaching unit of the Master of Bioinformatics of the University of Montpellier. Students take part in a research project analysing structural variants (SVs) and small nucleotide variants (SNVs).

They perform DNA extraction, sequencing, data analysis and interpretation of the results.

This pipeline starts by trimming the read files by removing reads smaller than 1,000 bp. It then proceeds to align the reads against the virus genomic reference. It processes the alignment by removing unaligned reads and converting them to a sorted binary format. It then performs a variant calling step and filters the resulting variants. Finally, it merges all variant files into a VCF file. Some statistical commands appear throughout the pipeline to check the quality of the data or results.

• Getting Started
  • Dependencies
  • How to install it
  • How to use it
• Authors
• Acknowledgements

• snakemake v7.21.0
• seqkit v2.3.0
• minimap2 v2.24-r1122
• samtools v1.16.1
• bamCoverage v3.5.1
• plotCoverage v3.5.1
• sniffles2 v2.2
• tabix v1.16
• bgzip v1.16
• bcftools v1.16
• medaka v1.11.3

Clone the repository wherever you want on your local:

git clone [email protected]:asfistonlavie/bill.git # by SSH 
git clone https://gitlab.com/asfistonlavie/bill.git # by HTTPS

Copy or move all your input data (reads and genomic references) to the resources/ folder (respectively resources/inputs/ and resources/references).

cp </path/to/your/reads/*.fastq> bill/resources/inputs/
cp </path/to/your/reads/*.fastq.gz> bill/resources/inputs/
cp </path/to/your/references/*.fasta> bill/resources/references/

There are three ways to use this pipeline: (1) by file name, (2) by file type, or (3) the whole pipeline. The main command to run all pipeline is snakemake --cores <nb_core_max>.

If you just want a specific file, run:

snakemake --cores <nb_core_max> <file_name>

It will automatically find the correct rule to run based on the file name. File names are constrained by the snakefile (see the wiki for correct file name format).

If you want all of a type of file, run :

snakemake --cores <nb_core_max> <file_type_name>

You can override each option in the configuration file- by adding the parameter --config <option_name>=<option_value> to the snakemake command.

Variant calling pipeline designed for the Bioinformatics Learning Lab (BILL: release_2023.1) A Soulier, A Arnoux, C Breton, E Cherif, AS Fiston-Lavier Zenodo. https://doi.org/10.5281/zenodo.10020027

• Arnaud Soulier Github profil
• Catherine Breton Github profil
• Emira Cherif Github profil
• Anna-Sophie Fiston-Lavier Github profil

We would like to thank the people involved in the BILL project, Jean-Christophe Avarre, Anne-Sophie Gosselin-Grenet and Marie-Ka Tilak, as well as all the students who took part in the project.