brentp

mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

cyvcf2

cython + htslib == fast VCF and BCF processing

vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

somalier

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

slivar

genetic variant expressions, annotation, and filtering for great good.

smoove

structural variant calling and genotyping with existing tools, but, smoothly.

goleft

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

hts-nim

nim wrapper for htslib for parsing genomics data files

echtvar

using all the bits for echt rapid variant annotation and filtering

bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome

jigv

igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"

vcfgo

a golang library to read, write and manipulate files in the variant call format.

vcfexpress

expressions on VCFs

fishers_exact_test

Fishers Exact Test for Python (Cython)

rare-disease-wf

(WIP) best-practices workflow for rare disease

geneimpacts

prioritize effects of variant annotations from VEP, SnpEff, et al.

fraguracy

overlapping bases in read-pairs from a fragment indicate accuracy and reveal error-prone sites

xvcf-rs

VCF/BCF [un]compressed [un]indexed

go-blosc

go wrapper for blosc (blocked number compression with fast random access)

bedder-rs

an API for intersections of genomic data

d4-nim

nim-lang wrapper for https://github.com/38/d4-format

svtyper

Bayesian genotyper for structural variants

nf-simple

fgoxide

Quality of life improvements in Rust.

perbase

Per-base per-nucleotide depth analysis

help-repositories

getting help on stuff.

hts-sys

Raw rust bindings for htslib

rust-bio

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

rust-htslib

This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.

vembrane-benchmark

benchmark workflow for vcfexpress paper