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abpoa

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band

bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

benchmarking_sv_publication

Updated figures for "A benchmarking of WGS-based structural variant callers" paper

bioconda-recipes

Conda recipes for the bioconda channel.

codeaxe

Model initially described in "Saunders CT, Green P. Insights from modeling protein evolution with context-dependent mutation and asymmetric amino acid selection."

detect_crt_static

error-stack-demo

expansionhunter

A tool for estimating repeat sizes

gatk

GATK fork with minor edits useful in creating gVCF output (in branch: "gvcf")

hap-eval

A VCF comparison engine for structual variant benchmarking

homebrew-science

:microscope: Scientific formulae for the Homebrew package manager

hts-specs

Specifications of SAM/BAM and related high-throughput sequencing file formats

htslib

C library for high-throughput sequencing data formats

igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

lua-filters

A collection of lua filters for pandoc

manta

Structural variant and indel caller for mapped sequencing data

memusg

A 'time'-like utility for Unix that measures peak memory usage

minimal_cxx

Minimal demonstration of cxx static build issue

pyflow

A lightweight parallel task engine

r4ds

R for data science: a book

rs-sandbox

rust-wfa2

Rust binding for WFA2-lib

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

sml_galign

Supporting ortholog scripts from "Saunders CT, Green P. Insights from modeling protein evolution with context-dependent mutation and asymmetric amino acid selection."

strelka

Strelka2 germline and somatic small variant caller

svtools

Tools for processing and analyzing structural variants.

tflite-rs

truvari

Structural variant toolkit for VCFs

vcf4sv

vcflib

a simple C++ library for parsing and manipulating VCF files, + many command-line utilities