Short Read Mappers

MAQhttp://maq.sourceforge.net
Bowtiehttp://bowtie-bio.sourceforge.net/index.shtml
BWAhttp://bio-bwa.sourceforge.net/bwa.shtml
Novoalignhttp://www.novocraft.com
SOAP2http://soap.genomics.org.cn
BFASThttps://secure.genome.ucla.edu/index.php/BFAST
Shrimphttp://compbio.cs.toronto.edu/shrimp
Mosaikhttp://bioinformatics.bc.edu/marthlab/Mosaik
SAMtoolshttp://samtools.sourceforge.net/Manipulating alignments in the SAM format
HTSeqhttp://www-huber.embl.de/users/anders/HTSeq/doc/overview.htmlPython package for sequencing data

Genome Browsers/Viewers

IGVhttp://www.broadinstitute.org/igv
UCSC Genome Browserhttp://genome.ucsc.edu/
CisGenome Browserhttp://biogibbs.stanford.edu/~jiangh/browser
SAMtools viewerhttp://samtools.sourceforge.net/tview.shtml
Lookseqhttp://www.sanger.ac.uk/resources/software/lookseq
Tablethttp://bioinf.scri.ac.uk/tablet/
MochiViewhttp://johnsonlab.ucsf.edu/sj/mochiview-start/
Savant Genome Browserhttp://compbio.cs.toronto.edu/savant/

RNA-Seq Tools

Tophathttp://tophat.cbcb.umd.edusplice mapping
SpliceMaphttp://biogibbs.stanford.edu/~kinfai/SpliceMap/splice mapping
Cufflinkshttp://cufflinks.cbcb.umd.edutranscript assembly
Scripturehttp://www.broadinstitute.org/software/scripture/transcriptome reconstruction
ABYSShttp://www.bcgsc.ca/platform/bioinfo/software/abysstranscriptome assembly
Oaseshttp://www.ebi.ac.uk/~zerbino/oases/transcriptome assembly
DEGseqhttp://www.bioconductor.org/packages/release/bioc/html/DEGseq.htmldifferential expression
EdgeRhttp://bioconductor.org/packages/release/bioc/html/edgeR.htmldifferential expression
GOseqhttp://www.bioconductor.org/packages/release/bioc/html/goseq.htmlGene Ontology analyser for RNA-seq
WebGestalthttp://bioinfo.vanderbilt.edu/webgestalt/ Gene Set Analysis Toolkit

ChIP-Seq Tools

QuESThttp://mendel.stanford.edu/sidowlab/downloads/quest
SISSRshttp://dir.nhlbi.nih.gov/papers/lmi/epigenomes/sissrs
MACShttp://liulab.dfci.harvard.edu/MACS/
PeakSeqhttp://archive.gersteinlab.org/proj/PeakSeq/
SWEMBL http://www.ebi.ac.uk/~swilder/SWEMBL/

Alternative Splicing Databases

ASTDhttp://www.ebi.ac.uk/astd/main.html
ExonMinehttp://www.imm.fm.ul.pt/exonmine
ASDBhttp://www.eurasnet.info/tools/asdatabasesAlternative Splicing Databases

Data Archive

Gene Expression Omnibushttp://www.ncbi.nlm.nih.gov/geo/
Array Expresshttp://www.ebi.ac.uk/microarray-as/ae/
Sequencing Reads Archivehttp://www.ncbi.nlm.nih.gov/sra

NGS Companies

Roche/454http://www.454.com/
Illuminahttp://www.illumina.com
ABI/SOLiDhttp://www.appliedbiosystems.com/
PacBiohttp://www.pacificbiosciences.com/
PacBioDevhttp://www.pacbiodevnet.com/

Related Journals

Naturehttp://www.nature.com/nature/index.html
Nature Biotechnologyhttp://www.nature.com/nbt/index.html
Nature Geneticshttp://www.nature.com/ng/index.html
Nature Review Geneticshttp://www.nature.com/nrg/index.html
Nature Methodshttp://www.nature.com/nmeth/index.html
Genome Researchhttp://genome.cshlp.org/
Genome Biologyhttp://genomebiology.com/
Nucleic Acids Researchhttp://nar.oxfordjournals.org/
PLoS Computational Biologyhttp://www.ploscompbiol.org/
Bioinformaticshttp://bioinformatics.oxfordjournals.org/
BMC Bioinformaticshttp://www.biomedcentral.com/bmcbioinformatics/
Genomicshttp://www.elsevier.com/locate/ygeno
Journal of Theoretical Biologyhttp://www.elsevier.com/locate/yjtbi
BBRChttp://www.elsevier.com/locate/ybbrc
Pubmedhttp://www.ncbi.nlm.nih.gov/pubmed/