SeMeta

SeMeta is a new software for taxonomic assignment of metagenomic reads. It supports both single-end and paired-end reads. The software is implemented in C++

Source codes:

Download source code here:
Version 1.0 (release 02/10/2015): SeMeta1.0.tar.gz
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
The application was tested with various datasets. The datasets can be downloaded here:
- Dataset 1: ds1.fna.gz
- Dataset 2: ds2.fna.gz
- Dataset 3: ds3.fna.gz
- Acid mine drainage: http://www.ncbi.nlm.nih.gov/books/NBK6860/
- Human gut metagenome: http://public.genomics.org.cn/BGI/gutmeta/

How to compile the source code, and prepare input files:

Please read the README.txt file in the source code folder.

Publications:

Vinh V. L., Lang V. T., and Hoai V. T. (2016). A novel semi-supervised algorithm for the taxonomic assignment of metagenomic reads. BMC Bioinformatics, 17 (22) (SCIE index, IF=2.58)

Other taxonomic assignment tools:

Megan5: http://ab.inf.uni-tuebingen.de/software/megan5/
Sort-ITEMS: http://metagenomics.atc.tcs.com/binning/SOrt-ITEMS/