Cite us
GATK PathSeq: Mark A Walker, Chandra Sekhar Pedamallu, Akinyemi I Ojesina, Susan Bullman, Ted Sharpe, Christopher W Whelan & Matthew Meyerson. GATK PathSeq: a customizable computational tool for the discovery and identification of microbial sequences in libraries from eukaryotic hosts. Bioinformatics, 34(24), 4287. https://doi.org/10.1093/bioinformatics/bty501
Original PathSeq: Aleksandar D Kostic, Akinyemi I Ojesina, Chandra Sekhar Pedamallu, Joonil Jung, Roel G W Verhaak, Gad Getz & Matthew Meyerson. PathSeq: software to identify or discover microbes by deep sequencing of human tissue. Nature Biotecnology, 29, 393-396, 2011. https://doi.org/10.1038/nbt.1868
Code:GATK Pathseq: https://github.com/broadinstitute/gatk
PathSeq v2.0: https://github.com/ChandraPedamallu/PathSeq