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.
PathSeq: software to identify or discover microbes by deep sequencing of human tissue
Nat Biotechnol. 2011 May;29(5):393-6.
Aleksandar D Kostic, Akinyemi I Ojesina, Chandra Sekhar Pedamallu, Joonil Jung, Roel G W Verhaak, Gad Getz & Matthew Meyerson
Genomic analysis identifies association of Fusobacterium with colorectal carcinoma
Genome Res. 2012. 22: 292-298
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