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bamtools

C++ API & command-line toolkit for working with BAM data

bioconda-recipes

Conda recipes for the bioconda channel.

bwa

Burrow-Wheeler Aligner

chromaclique

giab-phasing

Pipeline for haplotype phasing using Genome in a Bottle data

graph-genomics-review

Precision pangenomics (review article on graph genomics)

hgsvc_haplotyping_pipeline

integrativephasingpaper

Supplementary files for the study "Dense and accurate whole-chromosome haplotyping of individual genomes"

mosaicatcher

Processing of raw Strand-seq data as part of the SV calling pipeline

pyseqan

Python bindings for Seqan

simseq

An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries . Additionally the program provides the ability to model both site and base specific error, and scripts are provided to train this error model on real datasets. My hope in creating this program is to generate as realistic data as possible to assist in assessing the accuracy of genome assembly tools.

theupsetkmer

Create Upset diagrams from k-mer sets