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

bwa-meth

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

echtvar

using all the bits for echt rapid variant annotation and filtering

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.

fishers_exact_test

Fishers Exact Test for Python (Cython)

rare-disease-wf

(WIP) best-practices workflow for rare disease

tiwih

simple bioinformatics command-line (t)ools (i) (w)ished (i) (h)ad.

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

pbr

drunk on perbase pileups and lua expressions

spacepile

convert reads from repeated measures of same piece of DNA into spaced matricies for deep learners.

xvcf-rs

VCF/BCF [un]compressed [un]indexed

oodles

oodles of bioinformatics tools

go-blosc

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

bedder-rs

an API for intersections of genomic data

svtyper

Bayesian genotyper for structural variants

nf-simple

nim-minizip

nothing to see here.

fgoxide

Quality of life improvements in Rust.

perbase

Per-base per-nucleotide depth analysis

help-repositories

getting help on stuff.

rust-htslib

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