WeavePop: A bioinformatics workflow to explore and analyze genomic variants of eukaryotic populations

Abstract

Analyzing genomic variants in large datasets composed of short-read sequencing data is a process that requires multiple steps and computational tools, which makes it a complicated task that is difficult to reproduce across projects and laboratories. To address this need, we developed a reproducible and scalable Snakemake workflow called WeavePop, which aligns samples to selected references, obtains reference-based assemblies, annotations, and sequences, and identifies small variants and copy-number variants in eukaryotic haploid organisms. All the results are integrated into a database that can be easily shared and explored through a graphical web interface provided alongside the workflow, making the discovery of variants in a population of study very simple. WeavePop is available from GitHub (https://github.com/magwenelab/WeavePop) for Linux operating systems. Here we exemplify the use of WeavePop in a large collection of isolates of the pathogenic fungus Cryptococcus neoformans. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=187 SRC="FIGDIR/small/670593v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1b1bf6eorg.highwire.dtl.DTLVardef@8edae9org.highwire.dtl.DTLVardef@c60290org.highwire.dtl.DTLVardef@1d27bef_HPS_FORMAT_FIGEXP M_FIG C_FIG