Links

Babraham MolBio Software Repository

http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/
to download SeqMonk.

Links to other websites

Illumina, Inc.
The Genome Analyzer manufacturer’s website. Access to Product Documentation is limited, but they have an extensive list of journal references describing  the applications of Illumina technology in a range of research projects.

SeqAnswers
An invaluable site for users of Next Generation Sequencing Technologies, including news on NGS-related products and events, pages on the technologies on the market and user forums where you can post and answer your NGS questions.

Short Read Aligners

Bowtie – described as a fast and memory-efficient aligner. Developed by the CBCB, University of Maryland and Johns Hopkins. Hosted at SourceForge.

BWA – (Burrows-Wheeler Aligner) can align short or long reads. Developed by H. Li, hosted at SourceForge.

MAQ - (Mapping and Assembly with Qualities) a widely-used aligner (including at the Sanger Institute). Developed by H. Li, hosted at SourceForge.

Novoalign – A commercial software available as a free download for not-for-profit purposes/ research groups. Developed by Novocraft Technologies.

SOAPAligner/soap2  – part of the Short Oligonucleotide Analysis Package developed at the Beijing Genomics Institute.

Peak Calling Programs

FindPeaks – part of the Vancouver Short Read Analysis Project developed by A. Fejes and hosted at SourceForge.

MACS – (Model-based Analysis for ChIP-seq) developed at the Liu laboratory,
Dana-Farber Cancer Institute, Harvard.

PeakSeq -  developed by J. Rozowsky at the Gerstein Laboratory, Yale.

Histone Modifications and Chromatin Signatures

ChIPDiff—identification of Differential Histone Modification Sites (DHMSs) by comparing two ChIP-seq libraries. A Hidden Markov Model (HMM) is employed in ChIPDiff to infer the states of histone modification changes
Genome Institute of Singapore.

ChromaSig—a probabilistic approach to finding common chromatin signatures in the human genome
Ludwig Institute for Cancer Research.

Transcriptome Analysis

ERANGE— for both ChIP-seq and RNA-seq analyses.
Wold Lab, California Institute of Technology.

TopHat—fast splice junction mapper for RNA-seq reads.
CBCB, University of Maryland.

Bioconductor package edgeR—empirical analysis of digital gene expression data
Bioconductor, University of Michigan.

BayesSeq—Bayesian method based on Poisson or negative binomial distributions.
SIROCCO/University of Cambridge.

miRNA-seq

miRDeep—for discovering known and novel miRNA from deep sequencing data.
Systems Biology, Max Delbrűck Center, Berlin-Buch.