MetaObtainer

Software Package

Overview

MetaObtainer can (1) deal with next-generation sequencing reads which are shorter than 100bp with very high accuracy (both of Precision and Recall are more than 97%); (2) find unknown species using the reference genomes of species which are similar with it; (3) perform well when reads of specified species are very few in the dataset; (4) handle genomes of similar abundance levels as well as different abundance levels (1:10) .

Download

The software MetaObtainer is free for non-commercial use. Executables are available for download:

Program Usage

You can run the executables directly as follow:

$ ./metaobtainer [options]

options:

-r        Reads file (fasta).

-o        Output directory.

-k        Length of k-mers.

-c        information of reference genomes

Citation

If you use MetaObtainer in public, please cite the publication:
Pan, W., Chen, B. and Xu, Y., 2015. MetaObtainer: A Tool for Obtaining Specified Species from Metagenomic Reads of Next-generation Sequencing. Interdisciplinary Sciences: Computational Life Sciences,7(4), pp.405-413.

Contacts

Weihua Pan
Phone: (951)323-3581
Email: wpan005@ucr.edu
Office: 502, NHPCC(Hefei), USTC, Jinzhai Road
Homepage: http://www.cs.ucr.edu/~wpan005