Introduction

The determination of protein sequences from a metagenomic dataset enables the study of metabolism and functional roles of the organisms that are present in the sampled microbial community. We had previously introduced algorithm and software for the accurate reconstruction of protein sequences from short peptides identified on nucleotide reads in a metagenomic dataset. Here, we present significant computational improvements to the short peptide assembly algorithm that make it practical to reconstruct proteins from large metagenomic datasets containing several hundred million reads, while maintaining accuracy. The improved computational efficiency is achieved using a suffix array data structure that allows for fast querying during the assembly process, and a significant redesign of assembly steps that enables multi-threaded execution.The program is available under the GPLv3 license from sourceforge.net/projects/spa-assembler.

Publications

  1. SFA-SPA: a suffix array based short peptide assembler for metagenomic data.
    Cite this
    Yang Y, Zhong C, Yooseph S, 2015-06-01 - Bioinformatics (Oxford, England)

Credits

  1. Youngik Yang
    Developer

    Informatics Department, J. Craig Venter Institute, United States of America

  2. Cuncong Zhong
    Developer

    Informatics Department, J. Craig Venter Institute, United States of America

  3. Shibu Yooseph
    Investigator

    Informatics Department, J. Craig Venter Institute, United States of America

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Summary
AccessionBT001479
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++, Perl
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByShibu Yooseph