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Bioinformatics. 2013 Feb 1;29(3):391-2. doi: 10.1093/bioinformatics/bts684. Epub 2012 Nov 28.

READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation.

Author information

  • 1Pathogen Genomics Laboratory, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal-23955-6900, Kingdom of Saudi Arabia. raeece.naeem@gmail.com

Abstract

READSCAN is a highly scalable parallel program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. READSCAN accurately classified human and viral sequences on a 20.1 million reads simulated dataset in <27 min using a small Beowulf compute cluster with 16 nodes (Supplementary Material).

AVAILABILITY:

http://cbrc.kaust.edu.sa/readscan.

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