SEAL 0.4.0rc2 – Read Mapper and Duplicate Remover

SEAL 0.4.0rc2

:: DESCRIPTION

Seal is a suite of distributed applications for aligning short DNA reads, and manipulating and analyzing short read alignments. Seal applications generally run on the Hadoop framework and are made to scale well in the amount of computing nodes available and the amount of the data to process. This fact makes Seal particularly well suited for processing large data sets. Seal is part of the Biodoop suite of tools.

::DEVELOPER

Luca Pireddu, Simone Leo and Gianluigi Zanetti

:: SCREENSHOTS

N/A

: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SEAL

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Aug 1;27(15):2159-60. doi: 10.1093/bioinformatics/btr325.
SEAL: a distributed short read mapping and duplicate removal tool.
Pireddu L, Leo S, Zanetti G.

SOCS 2.2 – SOLiD Read Mapper with Bisulfite Sequencing Support

SOCS 2.2

:: DESCRIPTION

SOCS (short oligonucleotide color space) is a SOLiD read mapper with bisulfite sequencing support.SOCS performs ungapped alignment of SOLiD (color space) sequencing reads against reference sequences. Modes are available for detecting short sequence-space variants (such as SNPs) and for detecting unlimited numbers of bisulfite-induced nucleotide substitutions for 5mC methylation studies.

::DEVELOPER

Nicholas H. Bergman (nickbergman@gatech.edu)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 SOCS

:: MORE INFORMATION

Citation

An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System.
Ondov BD, Cochran C, Landers M, Meredith GD, Dudas M, Bergman NH.
Bioinformatics. 2010 Aug 1;26(15):1901-2. doi: 10.1093/bioinformatics/btq291.

Rabema 1.1 – Read Mappers

Rabema 1.1

:: DESCRIPTION

Rabema (Read Alignment BEnchMArk),is a program that supports a new read mapper benchmark methodology. The methodology is based on a strict definition of the read mapping problem and allows the evaluation of arbitrary read mapping programs that create SAM output.

::DEVELOPER

Rabema Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

  Rabema

:: MORE INFORMATION

Citation

M. Holtgrewe, A.-K. Emde, D. Weese and K. Reinert.
A Novel And Well-Defined Benchmarking Method For Second Generation Read Mapping,
BMC Bioinformatics 2011, 12:210, doi:10.1186/1471-2105-12-21.