Quality control
SolexaQA	http://solexaqa.sourceforge.net/
FastQC	http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/
Tag Mapping
Bowtie	http://bowtie-bio.sourceforge.net/index.shtml
SOAP2	http://soap.genomics.org.cn/
Peak Finding
DESQ	http://www-huber.embl.de/users/anders/DESeq/
USEQ	http://useq.sourceforge.net/
MACS	http://liulab.dfci.harvard.edu/MACS
Motif Finding
GimmeMotifs	http://www.ncmls.eu/bioinfo/gimmemotifs/
The MEME Suite	http://meme.sdsc.edu/meme
Annotation.
Affymetrix & NimbleGen gene expression microarray human-zebrafish orthologs	http://zfblast1.danio.tchlab.org/zgMap/ZGMAP.htm
Anno-J	http://www.annoj.org
DAVID	http://david.abcc.ncifcrf.gov
Gene Ontology	http://www.geneontology.org
GREAT	http://great.stanford.edu/public/cgi-bin/great.php
STRING	http://string-db.org
General
Bioconductor / R	http://www.bioconductor.org/
BioMart	www.biomart.org
The Cancer Genome Atlas	http://tcga.cancer.gov
ChromaSig	http://bioinformatics-renlab.ucsd.edu/rentrac/wiki/ChromaSig
CEAS	http://ceas.cbi.pku.edu.cn
CisGenome	http://www.biostat.jhsph.edu/~hji/cisgenome
Cytoscape	http://www.cytoscape.org
ENCODE Project	http://www.genome.gov/10005107
Entrez Genome	http://www.ncbi.nlm.nih.gov/sites/genome
Ensembl	http://www.ensembl.org
EpiGRAPH	http://epigraph.mpi-inf.mpg.de/WebGRAPH/
Galaxy	http://galaxy.psu.edu
Gene Set Enrichment Analysis	http://www.broadinstitute.org/gsea
NCBI	http://www.ncbi.nlm.nih.gov
NextBio	http://www.nextbio.com
NPG	http://www.sanger.ac.uk/resources/software/npg/
Peak Analyzer	http://www.bioinformatics.org/peakanalyzer/wiki/
Roadmap Epigenomics Project	http://www.roadmapepigenomics.org
SEQanswers	http://seqanswers.com/wiki/Software/list
UCSC Genome Browser	http://genome.ucsc.edu