Gabriel Renaud

deML. Maximum likelihood demultiplexing

gargammel. gargammel is an ancient DNA simulator

leeHom. Bayesian reconstruction of ancient DNA fragments

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

vgan. Suite of tools for pangenomics built using vg

schmutzi. Maximum a posteriori estimate of contamination for ancient samples

ROHan. Joint inference of heterozygosity rates and runs of homozygosity

freeIbis. An efficient basecaller for Illumina sequencers with calibrated quality scores

BCL2BAM2FASTQ. C++

SAFARI. Sensitive Alignments from a RYmer Index

aLib. Python

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

VCFparser. C++ library for parsing VCF files

mappability_snpable. Shell

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

trieFinder. The trieFinder program is designed to rapidly map Digital Gene Expression (DGE) tags of various lengths to RefSeq, UniGene, and/or genomic sequences. It annotates the tags with information from the sequence files, providing output in a format that is amenable to both transcript quantification and the detection of novel transcripts.

bam2prof. the subprogram in schmutzi but rewritten using htslib

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

cinch. Python

libgab. A C++ class of useful little functions

GenStat. C++

mitochondrialSimulator. A simple mitochondrial simulator

aligneur_sequence. C++