SUPER-FOCUS 0.34 – Agile Functional Analysis of Shotgun Metagenomic data

SUPER-FOCUS 0.34

:: DESCRIPTION

SUPER-FOCUS (SUbsystems Profile by databasE Reduction using FOCUS) an agile homology-based approach using a reduced SEED database to report the subsystems present in metagenomic samples and profile their abundances.

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • Python

:: DOWNLOAD

 SUPER-FOCUS

:: MORE INFORMATION

Citation:

SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data.
Silva GG, Green KT, Dutilh BE, Edwards RA.
Bioinformatics. 2015 Oct 9. pii: btv584.

AGILE 0.4.0 – AliGnIng Long rEads

AGILE 0.4.0

:: DESCRIPTION

AGILE is a sequence mapping tool specifically designed to map the longer reads (read length > 200) to a given reference genome. Currently it works for 454 reads, but efforts are being made to make it suitable to work for all sequencers, which produce longer reads. Looking at the current trend of increasing read lengths, soon most of the sequencers have read lengths > 200.

::DEVELOPER

Sanchit Misra

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 AGILE

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jan 15;27(2):189-95. Epub 2010 Nov 18.
Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencing.
Misra S, Agrawal A, Liao WK, Choudhary A.