metafast

MetaFast (METAgenome FAST analysis toolkit) is a toolkit for calculating a number of statistics of metagenome sequences and building the distance matrix between them.

Authors:

• Software: Sergey Kazakov and Vladimir Ulyantsev, ITMO University, Saint-Petersburg.
• Testing: Veronika Dubinkina and Alexandr Tyakht, SRI of Physical-Chemical Medicine, Moscow.
• Idea, supervisor: Dmitry Alexeev, SRI of Physical-Chemical Medicine, Moscow.

Installation

The last stable release can be downloaded from http://github.com/ctlab/metafast/releases.

To run metafast JRE 1.6 or higher is requered. Only one metafast script (metafast.sh, metafast.bat or metafast.jar) is requered to run metafast.

• For Linux and Mac OS: download metafast.sh, run the command chmod a+x metafast.sh, then run ./metafast.sh from the command line.
  
• For Windows: download metafast.bat and run it from the command line.
• For other OS: download metafast.jar and run it via command java -jar metafast.jar.

If you would like to build the last version of metafast from the repository (and check the version stamp):

git clone https://github.com/ctlab/metafast.git
cd metafast 
ant
./out/metafast.sh --version

Example

Download tinytest_A.fastq and tinytest_B.fastq and run the command:

./metafast.sh -k 7 -b 0 -l 8 -b1 3 -i tinytest_A.fastq tinytest_B.fastq

After it has finished, a distance matrix can be found in workDir/matrices/dist_matrix_<date>_<time>.txt:

#	tinytest_A.vec	tinytest_B.vec
tinytest_A.vec	0.0	0.09090909090909091
tinytest_B.vec	0.09090909090909091	0.0

The element matrix[i][j] is a distance between sample i and sample j.

K-mers frequency statistics is saved in workDir/kmer-counter-many/stats/<in-file>.stat.txt.

Full documentation

To see the full documentation visit http://github.com/ctlab/metafast/wiki.

See also

• khmer - a toolkit to split reads.
• crAss - Cross-Assembly of Metagenomes.
• MaryGold - Variation analysis of metagenomic samples.