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WeavePop: a bioinformatics workflow to explore and analyze genomic variants of eukaryotic populations
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DOI：10.1093/g3journal/jkag039.png)
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Abstract
En 中文
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.
Keywords:
copy number variants
small variants
population genomics
eukaryotic
Snakemake
shiny
database
workflow
fungi
Python
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