PathSeq

PathSeq is a computational tool for the identification and analysis of microbial sequences in high-throughput human sequencing data that is designed to work with large numbers of sequencing reads in a scalable manner.

Contact: 
pathseq-help@broadinstitute.org
Publication Info: 
Title: 
PathSeq: software to identify or discover microbes by deep sequencing of human tissue
Date: 
Nat Biotechnol. 2011 May;29(5):393-6.
Notes: 
Aleksandar D Kostic, Akinyemi I Ojesina, Chandra Sekhar Pedamallu, Joonil Jung, Roel G W Verhaak, Gad Getz & Matthew Meyerson
Title: 
Genomic analysis identifies association of Fusobacterium with colorectal carcinoma
Date: 
Genome Res. 2012. 22: 292-298
Notes: 
Aleksandar D. Kostic, Dirk Gevers, Chandra Sekhar Pedamallu, Monia Michaud, Fujiko Duke, Ashlee M. Earl, Akinyemi I. Ojesina, Joonil Jung, Adam J. Bass, Josep Tabernero, José Baselga, Chen Liu, Ramesh A. Shivdasani, Shuji Ogino, Bruce W. Birren, Curtis Huttenhower, Wendy S. Garrett, and Matthew Meyerson