Collection of tools for next generation sequencing (NGS) analysis of whole genome/exome/transcriptome data (not comprehensive)
General tools/recommendations
Unix
Perl/Python/bash scripting
R for statistical analysis
Quality control
FastQC http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Read trimming (and adaptor removal)
Trimmomatic http://www.usadellab.org/cms/?page=trimmomatic
ConDeTri https://github.com/linneas/condetri
FASTX-Toolkit http://hannonlab.cshl.edu/fastx_toolkit/
cutadapt https://github.com/marcelm/cutadapt
BBDuk https://sourceforge.net/projects/bbmap/
Error correction
Quake http://www.cbcb.umd.edu/software/quake/
Echo http://uc-echo.sourceforge.net/
BBNorm https://sourceforge.net/projects/bbmap/
Short read aligner
bwa https://github.com/lh3/bwa
bowtie http://bowtie-bio.sourceforge.net/index.shtml
BBMap https://sourceforge.net/projects/bbmap/
Stampy http://www.well.ox.ac.uk/project-stampy
segemehl http://www.bioinf.uni-leipzig.de/Software/segemehl/
RNA-seq aligner
HISAT2 http://ccb.jhu.edu/software/hisat2/index.shtml
STAR https://github.com/alexdobin/STAR
Tophat2 http://ccb.jhu.edu/software/tophat/index.shtml
Pseudo-aligner for RNA-seq
kallisto https://pachterlab.github.io/kallisto/
Salmon https://combine-lab.github.io/salmon/
Sailfish http://www.cs.cmu.edu/~ckingsf/software/sailfish/
Variant calling
GATK https://software.broadinstitute.org/gatk/gatkdocs/current/
VarScan2 http://dkoboldt.github.io/varscan/
Samtools http://www.htslib.org/
FreeBayes https://github.com/ekg/freebayes
VarDict https://github.com/AstraZeneca-NGS/VarDict
Variant annotation
ANNOVAR https://github.com/WGLab/doc-ANNOVAR/
Oncotator http://portals.broadinstitute.org/oncotator/
SNPeff http://snpeff.sourceforge.net/index.html
VAT http://vat.gersteinlab.org/
VeP http://www.ensembl.org/info/docs/tools/vep/index.html
CADD http://cadd.gs.washington.edu/
Condel http://bg.upf.edu/fannsdb/query/condel
CGI https://www.cancergenomeinterpreter.org/home
Manipulating files (sam/bam/vcf/gff/gtf/...)
Picard tools http://broadinstitute.github.io/picard/
Samtools http://www.htslib.org/
BCFtools http://www.htslib.org/
bedtools http://bedtools.readthedocs.io/en/latest/
BamTools https://github.com/pezmaster31/bamtools
bam-readcount https://github.com/genome/bam-readcount
BBTools http://jgi.doe.gov/data-and-tools/bbtools/
Fusion genes
JAFFA https://github.com/Oshlack/JAFFA
DeFuse http://compbio.bccrc.ca/software/defuse/
EricScript https://sites.google.com/site/bioericscript/
pizzly https://github.com/pmelsted/pizzly
Quantitative analysis/Differential expression
sleuth http://pachterlab.github.io/sleuth/
limma http://bioconductor.org/packages/release/bioc/html/limma.html
DESeq2 http://bioconductor.org/packages/release/bioc/html/DESeq2.html
edgeR http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
Visualisation
IGV http://software.broadinstitute.org/software/igv/
IGB http://bioviz.org/igb/
UCSC Genome browser
Genome builds
Coming soon