HPCBIOS_2012-94: Bioinformatics & Comp. Biology Productivity Environment

Note

Bioinformatics & Computational Biology productivity environment includes a set of HPC tools which are needed for scientific computing and visualization in the respective domain. The following is an attempt to define which ones are relevant for the HPCBIOS communities and set an action plan.

• BC Policy: HPCBIOS_2012-94
• Date of Policy: 2013-12-22

The main objective of this policy is to provide the following common productivity environment across any HPCBIOS resources:

Name	Prefered version(s)	Compliance level	Reference URL
Python	v2.7.3	MUST	http://www.python.org/
Biopython	1.61	MUST	http://biopython.org
scipy	0.10.1	MUST	http://www.scipy.org
numpy	1.6.1	MUST	http://numpy.scipy.org
Cython	0.16	MUST	http://pypi.python.org/pypi/Cython/
R language	v2.14.2 or v3.2.x or later	SHOULD	http://www.r-project.org
Bioconductor	v2.10	SHOULD	http://www.bioconductor.org
Perl	v5.16.3	MUST	http://www.perl.org/
BioPerl	1.6.1	MUST	http://www.bioperl.org/
NCBI-Toolkit	9.0.0	MUST	http://www.ncbi.nlm.nih.gov/toolkit
BLAST+	v2.2.26 or later	MUST	http://blast.ncbi.nlm.nih.gov/
mpiBLAST	v1.6.0	MUST	http://www.mpiblast.org/
HMMER	v3	MUST	http://hmmer.janelia.org/
MrBayes	v3.1.2	MUST	http://mrbayes.sourceforge.net
AMOS	3.1.0	MUST	http://sourceforge.net/apps/mediawiki/amos
Boost	1.49 or later	MUST	http://www.boost.org
Bowtie2	2.0.2	MUST	http://bowtie-bio.sourceforge.net/bowtie2
BWA	0.6.2	MUST	http://bio-bwa.sourceforge.net
ClustalW2	2.1	MUST	http://www.ebi.ac.uk/Tools/msa/clustalw2
Cufflinks	2.0.2	MUST	http://cufflinks.cbcb.umd.edu
Eigen	3.1.1	MUST	http://eigen.tuxfamily.org/index.php?title=Main_Page
FASTX-Toolkit	0.0.13.2	MUST	http://hannonlab.cshl.edu/fastx_toolkit
libgtextutils	0.6.1	MUST	http://hannonlab.cshl.edu/fastx_toolkit
Infernal	1.1	MUST	http://infernal.janelia.org
MUMmer	3.23	MUST	http://mummer.sourceforge.net
MetaVelvet	1.2.01	MUST	http://metavelvet.dna.bio.keio.ac.jp
RNAz	2.1	MUST	http://www.tbi.univie.ac.at/~wash/RNAz
SOAPdenovo	1.05	MUST	http://soap.genomics.org.cn/index.html
SAMtools	0.1.18	MUST	http://samtools.sourceforge.net
TopHat	2.0.4	MUST	http://tophat.cbcb.umd.edu
ViennaRNA	2.0.7	MUST	http://www.tbi.univie.ac.at/~ronny/RNA/vrna2.html
Velvet	1.2.07	MUST	http://www.ebi.ac.uk/~zerbino/velvet
BFAST	0.7.0a	MUST	http://bfast.sourceforge.net/
MCL	12.135	MUST	http://micans.org/mcl/
MEME	4.8.0	MUST	http://meme.nbcr.net/
HH-suite	2.0.16	MUST	ftp://toolkit.lmb.uni-muenchen.de/HH-suite/
BLAT	3.5	MUST	http://genome.ucsc.edu/FAQ/FAQblat.html
MUSCLE	3.8.31	MUST	http://www.drive5.com/muscle/
EMBOSS	6.5.7	MUST	http://emboss.sourceforge.net/
GATK	2.6-5 or later	MUST	http://www.broadinstitute.org/gatk/
PLINK	1.07	MUST	http://pngu.mgh.harvard.edu/purcell/plink/
CD-HIT	4.5.5	MUST	http://weizhong-lab.ucsd.edu/cd-hit/
RAxML	7.7.5 or later	MUST	https://github.com/stamatak/standard-RAxML
Oases	0.2.08	MUST	http://www.ebi.ac.uk/~zerbino/oases
Glimmer	3.0.2	MUST	http://ccb.jhu.edu/software/glimmer
PANDAseq	2.5	MUST	https://github.com/neufeld/pandaseq
ABySS	1.3.4	MUST	http://www.bcgsc.ca/platform/bioinfo/software/abyss
ALLPATHS-LG	46968	MUST	http://www.broadinstitute.org/software/allpaths-lg/blog/
ARB	5.5	MUST	http://www.arb-home.de/
bam2fastq	1.1.0	MUST	http://www.hudsonalpha.org/gsl/information/software/
BamTools	2.2.3	MUST	https://github.com/pezmaster31/bamtools
BEDTools	2.17.0	MUST	http://code.google.com/p/bedtools/
BiSearch	20051222	MUST	http://bisearch.enzim.hu/
Bowtie	1.1.0	MUST	http://bowtie-bio.sourceforge.net/index.shtml
CAP3	20071221	MUST	http://seq.cs.iastate.edu/
cutadapt	1.3	MUST	http://code.google.com/p/cutadapt/
FASTA	36.3.5e	MUST	http://fasta.bioch.virginia.edu
fastahack	20110215	MUST	https://github.com/ekg/fastahack
FoldX	2.5.2	MUST	http://http://foldx.crg.es/
FRC_align	20130521	MUST	https://github.com/vezzi/FRC_align
FreeSurfer	2.5	MUST	http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki
FSL	4.1.9	MUST	http://www.fmrib.ox.ac.uk/fsl/
GLIMMER	3.02b	MUST	http://www.cbcb.umd.edu/software/glimmer/
Mothur	1.30.2	MUST	http://www.mothur.org/
orthomcl	2.0.8	MUST	http://orthomcl.org/
PAML	4.7	MUST	http://abacus.gene.ucl.ac.uk/software/paml.html
PASHA	1.0.3	MUST	http://pasha.sourceforge.net/
Picard	1.100	MUST	http://picard.sourceforge.net/
Primer3	2.3.0	MUST	http://primer3.sourceforge.net
RNAz	2.1	MUST	http://www.tbi.univie.ac.at/~wash/RNAz
SHRiMP	2.2.3	MUST	http://compbio.cs.toronto.edu/shrimp/
Stacks	1.03	MUST	http://creskolab.uoregon.edu/stacks/
Stride	1.0	MUST	http://structure.usc.edu/stride/
SURF	1.0	MUST	http://www.ks.uiuc.edu/Research/vmd/vmd-1.7/ug/node65.html
Trinity	2013-02-25	MUST	http://trinityrnaseq.sourceforge.net/
IDBA-UD	1.1.1	SHOULD	http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud
Ruby	v1.9.3-p194 or later	SHOULD	http://www.python.org/
HOMER	4.2	SHOULD	http://homer.salk.edu/homer/
PhyML	latest	SHOULD	http://www.atgc-montpellier.fr/phyml/
Clustal	latest	SHOULD	http://www.clustal.org/
PyMOL	latest	SHOULD	http://pymol.sf.net/
FastQC	0.10.0	SHOULD	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

---

Future potential candidates for this policy:

T-Coffee	latest	SHOULD	http://www.tcoffee.org/
GPU-BLAST	latest	SHOULD	http://eudoxus.cheme.cmu.edu/gpublast/gpublast.html
CUDA-BLASTP	latest	SHOULD	https://sites.google.com/site/liuweiguohome/software
mpiCUDA-BLASTP	latest	SHOULD	https://sites.google.com/site/liuweiguohome/mpicuda-blastp
mr-mpi-blast	latest	SHOULD	https://github.com/andreyto/mr-mpi-blast
BioRuby	latest	SHOULD	http://bioruby.org
PolyPhen-2	2.2.2r405	SHOULD	http://genetics.bwh.harvard.edu/pph2/dokuwiki/start
SSAHA	31c	SHOULD	http://www.sanger.ac.uk/resources/software/ssaha/
RepeatMasker	latest	SHOULD	http://www.repeatmasker.org/
ABC-SysBio	latest	SHOULD	http://sourceforge.net/projects/abc-sysbio/
Annovar	latest	SHOULD	http://www.openbioinformatics.org/annovar/
PEMer	latest	SHOULD	http://sv.gersteinlab.org/pemer/
deFuse	latest	SHOULD	http://defuse.sf.net/
TopHat-Fusion	latest	SHOULD	http://tophat.cbcb.umd.edu/fusion_index.html
BreakDancer	latest	SHOULD	http://breakdancer.sourceforge.net/
PANTHER	latest	SHOULD	http://www.pantherdb.org/tools/
HHPRED	latest	SHOULD	http://toolkit.lmb.uni-muenchen.de/hhpred
pysam	latest	SHOULD	http://code.google.com/p/pysam/
ReadSeq	latest	SHOULD	http://iubio.bio.indiana.edu/soft/molbio/readseq/java/
Phrap	latest	SHOULD	http://www.phrap.org/phredphrapconsed.html
Phred	latest	SHOULD	http://www.phrap.org/phredphrapconsed.html
Consed	latest	SHOULD	http://www.phrap.org/consed/consed.html
nesoni	latest	SHOULD	http://bioinformatics.net.au/software.nesoni.shtml
galaxy	>ca0c4ad2bb39	SHOULD	http://galaxy.psu.edu/
swarm	latest	SHOULD	http://biowulf.nih.gov/apps/swarm.html /download/swarm.tar
WU-BLAST	latest	SHOULD	http://blast.wustl.edu/
PAUP	latest	SHOULD	http://paup.csit.fsu.edu/
PHYLIP	latest	SHOULD	http://evolution.genetics.washington.edu/phylip.html
QuEST	2.4	SHOULD	http://mendel.stanford.edu/sidowlab/downloads/quest/

This productivity environment will be supplemented with other related productivity tools as they become available on allocated systems.

Potential sources of information for further future upgrades of this list include:

• http://www.vital-it.ch/software/tools.php
• http://wiki.hpc.ufl.edu/doc/Category:Bioinformatics
• http://www.csc.fi/english/research/sciences/bioscience/programs/index_html
• http://bacpathgenomics.wordpress.com/software/
• http://umbc.rnet.missouri.edu/general/software/alphabetical.html
• http://www.broadinstitute.org/software/bsi-sig/
• http://ncgas.org/software, genome assembly, assembly, genomics
• http://confluence.rcs.griffith.edu.au:8080/display/GHPC/qiime#qiime-Alignment%2Ctreebuilding%2Ctaxonomyassignment%2COTUpicking%2Candotherdatagenerationsteps%28requiredforalternativepipelines%29
• http://www.bioplexity.org/lectures/ebi-s10.pdf
• http://helix.nih.gov/Applications/
• http://openwetware.org/wiki/Image:Tools.png
• http://en.wikipedia.org/wiki/List_of_sequence_alignment_software
• http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
• http://www.eaglegenomics.com/2012/04/the-elements-of-bioinformatics/
• http://nebc.nerc.ac.uk/tools/bio-linux-5/package-list

Kindly notify -if this policy is inadequate for your work- both your local site technical representative & HPCBIOS maintainers.