mi-faser is a metagenome (metagenome/metatranscriptome)
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-
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://email@example.com/bromberglab/mifaser_base.git
or download the zipped version:
curl --remote-name https://bitbucket.org/bromberglab/mifaser_base/get/master.zip unzip master.zip
Standalone VS Web Service
The Standalone version of mi-faser partitions the user input into subsets analogue to the Web Service (http://services.bromberglab.org/mifaser/). However, those partitions are processed sequentially and not in parallel as in the Web Service. Thus the Standalone Version is only recommended for smaller jobs and is mainly thought to provide the *mi-faser* code base.
Support online material for mi-faser manuscript: