Pinned Repositories
aLib
BCL2BAM2FASTQ
deML
Maximum likelihood demultiplexing
freeIbis
An efficient basecaller for Illumina sequencers with calibrated quality scores
gargammel
gargammel is an ancient DNA simulator
glactools
command-line tools for the management of genotype likelihoods and allele counts
leeHom
Bayesian reconstruction of ancient DNA fragments
ROHan
Joint inference of heterozygosity rates and runs of homozygosity
schmutzi
Maximum a posteriori estimate of contamination for ancient samples
vgan
Suite of tools for pangenomics built using vg
grenaud's Repositories
grenaud/freeIbis
An efficient basecaller for Illumina sequencers with calibrated quality scores
grenaud/aLib
grenaud/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.
grenaud/VCFparser
C++ library for parsing VCF files
grenaud/mitochondrialSimulator
A simple mitochondrial simulator
grenaud/arrayDesign
grenaud/bamtools
C++ API & command-line toolkit for working with BAM data
grenaud/bedBamAndBeyond
grenaud/BetaScan
Genome-wide scan for balancing selection using beta statistic
grenaud/dist2nj
transform the distance output from glactools into a neighbor joining tree
grenaud/fastautils
Little programs to handle fasta files
grenaud/GenStat
grenaud/grenaud
grenaud/GRoSS
Graph-aware Retrieval of Selective Sweeps
grenaud/mistartools
A set of programs for the management of allele count information on a per individual or population basis
grenaud/Mutation-Simulator
Mutation-Simulator is a tool designed to simulate mutations on given fasta files and creating an according vcf or csv file, which contains all information about the mutations.
grenaud/network-aware-bwa
Udo's networked BWA
grenaud/phasedVCF2ChromoPainter
Transform phased VCF into chromopainter
grenaud/piledriver
Basic, no assumptions, multi-pileup
grenaud/SimpleJSON
SimpleJSON is a simple JSON library written in C++. It is designed to be simple to use and be cross platform.
grenaud/splitdgm
little program to split dgm files from Ohana
grenaud/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
grenaud/stripAdaptersFQ2BAM
grenaud/tabixpp
C++ wrapper to tabix indexer
grenaud/uniqueBloom
Output unique DNA reads
grenaud/VCFShark