mi-faser

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mi-faser is a metagenome (metagenome/metatranscriptome) analysis tool developed by Chengsheng Zhu in the BrombergLab @ Rutgers University. The method was significantly sped up and made publicly available by Maximillian Miller (BrombergLabRutgers University and Rostlab @ Technical University of Munich).

mi-faser combines faser (functional annotation of sequencing reads), an algorithm that maps reads to molecular functions encoded by the read-correspondent genes, with a manually curated reference database of protein functions. As our method is optimized for short reads, no pre-assembly is required -- just submit your raw (but quality controlled) raw data AS IS.

As output, mi-faser produces high precision sets of molecular functions identified in the microbiome sequence data. mi-faser's minutes-per-microbiome processing speed is significantly faster than that of other annotation methods (less than 20min/10GB of reads), allowing for large scale comparisons. For instance, microbiome function vectors can be compared between different conditions or time-steps to highlight environment-specific and/or time-dependent changes in functionality.

Note that although mi-faser is specifically targeted to microbiome analysis, it could also potentially be used for the analysis of unassembled bacterial genome data as well.

Repository for source code and stand-alone version (linux/osx): https://bitbucket.org/bromberglab/mifaser_base

mifaser runs on LINUX, MacOSX and WINDOWS systems.

Open a terminal and checkout the mi-faser repository:

git clone https://git@bitbucket.org/bromberglab/mifaser_base.git

or download the zipped version:

curl --remote-name https://bitbucket.org/bromberglab/mifaser_base/get/master.zip
unzip master.zip

 

Support online material for mi-faser manuscript:

SOM Data S1. Multi-FASTA file of all the proteins in GS-set.

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