USeq 9.2.3 – Analyze Next Generation Sequencing data from Illumina, SOLiD, and 454 platforms

USeq 9.2.3

:: DESCRIPTION

USeq is a collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms. Initial emphasis: chIP-seq and RNA-Seq with FDR estimations.

::DEVELOPER

Huntsman Cancer Institute in the Utah Bioinformatics Shared Resource Center.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 USeq

:: MORE INFORMATION

Citation:

Nix DA, Courdy SJ, Boucher KM:
Empirical methods for controlling false positives and estimating confidence in chIP-seq peaks.
BMC Bioinformatics. 2008 Dec 5;9(1):523.

SToRM 0.0099 – Seed-based Read Mapping tool for SOLiD or Illumina sequencing data

SToRM 0.0099

:: DESCRIPTION

SToRM is a software tool primarily proposed for mapping SOLiD reads or Illumina reads to a reference genome. It was based on seeding techniques adapted to the statistical characteristics of the reads: the default seeds are for example designed (using the Iedera software) to comply with the properties of the SOLiD color encoding, or Illumina more classical encoding as well as the observed reading error distribution along the read.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux / MacOsX
  • C Compiler

:: DOWNLOAD

 SToRM

:: MORE INFORMATION

Citation

Noé, L. and Gîrdea,. and Kucherov, G.:
Designing efficient spaced seeds for SOLiD read mapping
Advances in Bioinformatics, Volume 2010 2010

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.

miRNA-MATE – A mapping pipeline for SOLiD miRNA data

miRNA-MATE

:: DESCRIPTION

miRNA-MATE is a package designed specifically for mapping and summarizing miRNA (and isomiR) data from SOLiD sequencing data sets. MicroRNAs can be particularly challenging to map because of the limited information content in a 22nt molecule.

::DEVELOPER

Expression Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • Java

:: DOWNLOAD

 miRNA-MATE

:: MORE INFORMATION

Citation

Nicole Cloonan,et al.
MicroRNAs and their isomiRs function cooperatively to target common biological pathways.
Genome Biology 2011, 12:R126

PerM 0.4.0 – Read-mapping software based on Periodic Spaced Seeds for both Illumina and SOLiD sequencing data

PerM 0.4.0

:: DESCRIPTION

PerM is a software package which was designed to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms. Today PerM is capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads.

::DEVELOPER

Ting Chen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 PerM

:: MORE INFORMATION

Citation:

Yangho Chen, Tade Souaiaia and Ting Chen
PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds
Bioinformatics (2009) 25 (19): 2514-2521.