Software list
bedtools2 (
http://bedtools.readthedocs.io/en/latest/
)
bowtie2 (
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
)
bwa (
http://bio-bwa.sourceforge.net/
)
cutadapt (
https://pypi.python.org/pypi/cutadapt
)
FastQC (
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
)
GenomeAnalysisTK (
https://software.broadinstitute.org/gatk/
)
HTSeq-count (
https://pypi.python.org/pypi/HTSeq
)
IGV (
http://software.broadinstitute.org/software/igv/
)
picard tools (
https://broadinstitute.github.io/picard/
)
samtools (
http://www.htslib.org/
)
tophat-2 (
https://ccb.jhu.edu/software/tophat/index.shtml
)