ClairS - a deep-learning method for long-read somatic small variant calling
ClairS-TO - a deep-learning method for tumor-only somatic variant calling
Generic human DNA variant annotation pipeline
Filters for Next Generation Sequencing
A collection of Python modules equivalent to R ReQTL Toolkit aims to identify the association between expressed SNVs with their gene expression using RNA-sequencing data.
A collection of software to work with genomic variants
A snakemake pipeline that performs variant calling of Nanopore reads from FastQ files for non-model organisms
A somatic mutation signature simulator
Determine read depth and variant frequency thresholds to distinguish NGS sequencing errors from true SNPs. Simulates effect of changing per-site read depth and variant frequency on accuracy of genetic diversity measures (pi, alterante allele frequency, shannon diversity).
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