Table 2.

Current list of analysis tools included and maintained on the Bioinformatics Training Platform. These tools are automatically configured and installed on the BTP images and instances

Tool	Function	Link
AMOS Hawkeye	Genome data visualization	http://sourceforge.net/projects/amos/
BEDTools	Genome data manipulation	http://bedtools.readthedocs.org/en/latest/
BLAT	Sequence location lookup in the genome	https://genome.ucsc.edu/FAQ/FAQblat.html
Bowtie	Read Alignment	http://bowtie-bio.sourceforge.net/index.shtml
CummeRbund	RNA-Seq analysis using R	http://bioconductor.org/packages/release/bioc/html/cummeRbund.html
Cufflinks	RNA-Seq analysis	http://cole-trapnell-lab.github.io/cufflinks/
DESeq2	Differential gene expression analysis using R	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
edgeR	Empirical gene expression analysis using R	https://bioconductor.org/packages/release/bioc/html/edgeR.html
FastQC	FastQC	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
FASTX	Toolkit for short reads preprocessing	http://hannonlab.cshl.edu/fastx_toolkit/
IGV	Interactive exploration of genomic data	https://www.broadinstitute.org/igv/
igvtools	For preprocessing data before loading to IGV	https://www.broadinstitute.org/igv/igvtools
MACS	ChIP-Seq analysis	http://liulab.dfci.harvard.edu/MACS/
MUMmer	Rapid genome alignment, a dependency for AMOS	http://mummer.sourceforge.net/
PeakAnalyzer	Multi-peak data analysis	http://www.bioinformatics.org/peakanalyzer/wiki/
Picard	Sequence data analysis	http://broadinstitute.github.io/picard/
SAMtools	For manipulating alignments in the SAM format	http://samtools.sourceforge.net/
Skewer	Adapter trimmer for paired-end reads	https://github.com/relipmoc/skewer