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/)