SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences
SOrt-ITEMS is a similarity based binning method. User needs to perform a similarity search of the input metagenomic sequences (reads) against the nr database using BLAST. The generated blastx output (corresponding to the metagenomic reads) is then taken as the input by SOrt-ITEMS program.
SYSTEM REQUIREMENTS :
1. Linux: Fedora (version 6 or higher) (Also works in Ubuntu 7 or higher)
2. Perl (version 5.8 or higher) and python should be installed and working.
3. Memory Requirement: 1 GB RAM or higher.
REFERENCE :
If you use SOrt-ITEMS please cite:
SOrt-ITEMS : Sequence Orthology based approach for binning and Improved
Taxonomic Estimation of Metagenomic Sequences.
Monzoorul Haque M, Tarini Shankar Ghosh, Dinakar Komanduri, and Sharmila S Mande
Bioinformatics 2009 25(14):1722-1730; doi:10.1093/bioinformatics/btp317
QUESTIONS, COMMENTS, SUGGESTIONS & BUG REPORTS :
To be reported to monzoor@atc.tcs.com (or) tarini@atc.tcs.com (or) dinakar.kbn@atc.tcs.com (or) sharmila@atc.tcs.com
CONTENTS AND COPYRIGHT :
This software contains the source executable and associated database files required for executing SOrt-ITEMS. All files are copyrighted, but license is hereby granted STRICTLY for academic, and non-profit use. Commercial users should contact Dr. Sharmila Mande at sharmila@atc.tcs.com
Copyright(c)2009. All rights reserved Tata Consultancy Services Limited
Bio-Sciences Division, Innovation Laboratory,
Tata Consultancy Services Limited,
1 Software Units Layout, Madhapur, Hyderabad 500 081, Andhra Pradesh, India.