Genome browsers
UCSC genome browser (https://genome.ucsc.edu/)
Ensembl (http://www.ensembl.org/index.html)
XGSC genome browser (http://www.xiphophorus.txstate.edu/genomeviewer.html)
Quality control tool
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Fastx_tools (http://hannonlab.cshl.edu/fastx_toolkit/)
Assembler
ALLPATHS (https://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12)
Trinity (https://github.com/trinityrnaseq/trinityrnaseq/wiki)
Velvet (https://www.ebi.ac.uk/~zerbino/velvet/)
Oases (https://www.ebi.ac.uk/~zerbino/oases/)
Cufflinks (http://cole-trapnell-lab.github.io/cufflinks/)
Celera Assembler/ Canu (For PacBio sequencing http://canu.readthedocs.io/en/stable/)
Celera Assembler/PBcR (For PacBio sequencing http://wgs-assembler.sourceforge.net/wiki/index.php?title=Main_Page)
MHAP (For PacBio sequencing http://mhap.readthedocs.io/en/stable/)
Quiver/Arrow polishing tool (https://github.com/PacificBiosciences/GenomicConsensus)
Aligner
MAQ (http://maq.sourceforge.net/maq-man.shtml)
Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
Tophat2 (https://ccb.jhu.edu/software/tophat/manual.shtml)
STAR (https://github.com/alexdobin/STAR)
Rsem (http://deweylab.biostat.wisc.edu/rsem/README.htmls)
GSNAP/GMAP (http://research-pub.gene.com/gmap/src/README)
Variation analysis/Genotyping
Samtools (http://samtools.sourceforge.net/)
Vcftools (http://vcftools.sourceforge.net/)
Varscan (http://varscan.sourceforge.net/)
GATK (https://www.broadinstitute.org/gatk/)
Gene expression quantification
Cufflinks (http://cole-trapnell-lab.github.io/cufflinks/)
Feature counts (http://bioinf.wehi.edu.au/featureCounts/)
Express (http://bio.math.berkeley.edu/eXpress/index.html)
HTSeq (http://www-huber.embl.de/HTSeq/doc/overview.html)
Statistical analysis packages
EdgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html)
DESeq2 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html)
Cuffmerge-Cuffdiff (http://cole-trapnell-lab.github.io/cufflinks/cuffmerge/)
Data bases
Gene Ontology (http://geneontology.org/)
SNPdb (http://www.ncbi.nlm.nih.gov/snp)
KEGG pathway (http://www.genome.jp/kegg/pathway.html)
ENCODE (https://www.encodeproject.org/)
1000 Genome Project (http://www.1000genomes.org/analysis)
The Cancer Genome Atlas (TCGA; http://cancergenome.nih.gov/)
Genomic Data Commons (https://gdc.nci.nih.gov/)