blahah/seqahead_software.md

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TGAC SeqAhead software requirements

Raw

seqahead_software.md

List of software to be pre-installed on VMs for SeqAhead course.

Transcriptome optimisation

RVM with latest Ruby (http://rvm.io/ - to install: \curl -sSL https://get.rvm.io | bash -s stable --ruby).
BLAST+ (latest version)
Bowtie2 (latest version)
CD-HIT (http://www.bioinformatics.org/project/filelist.php?group_id=350)
eXpress 1.5.1 (http://bio.math.berkeley.edu/eXpress/overview.html)
SoapDenovoTrans, fixed version from GitHub (https://github.com/cboursnell/SOAPdenovo-Trans)

Genome annotation

Maker 2.31 (http://www.yandell-lab.org/software/maker.html)
Apollo Genome Browser (http://genomearchitect.org/desktop-apollo)
InterProScan 5 (ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.3-46.0/)

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