grenaud

deML

Maximum likelihood demultiplexing

glactools

command-line tools for the management of genotype likelihoods and allele counts

gargammel

gargammel is an ancient DNA simulator

leeHom

Bayesian reconstruction of ancient DNA fragments

schmutzi

Maximum a posteriori estimate of contamination for ancient samples

vgan

Suite of tools for pangenomics built using vg

ROHan

Joint inference of heterozygosity rates and runs of homozygosity

dice

Joint estimate of demography and contamination for nuclear ancient DNA

DNA2INT

quick benchmarking to check the best way to transform DNA letters to integers

baselengthFilter

This program reads a BAM and produces another with a length filter applied on reads

insertsize

Simple C++ program built using samtools to get the insert size from BAM files

bam2prof

the subprogram in schmutzi but rewritten using htslib

cinch

libgab

A C++ class of useful little functions

mappability_snpable

mitochondrialSimulator

A simple mitochondrial simulator

bibtexFixCaps

Fix the capitalization problems for bibtex.

bioconda-recipes

Conda recipes for the bioconda channel.

bowtie2

A fast and sensitive gapped read aligner

epoParser

This program an EPO alignment index and fasta index for the genome and produces a tab delimited output

grenaud.github.io

ISBArch.github.io

Website for the International Society for Biomolecular Archaeology

libbam

Library of various programs based on bamtools

namedPipes

plass

Protein-Level ASSembler (PLASS): sensitive and precise protein assembler

redirectSTDout

staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

star_trek_linguistics

Did the quality of English go down in Star Trek transcripts?

testC-Obj

minimal code to learn C++ objects

vg

tools for working with genome variation graphs