NBIC & VIB Bioinformatics RPM Repository

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Goal

NBIC and BITS (Bioinformatics facility of the VIB, http://www.bits.vib.be) are maintaining both Galaxy servers focusing on NGS data analysis. To ease administration on their servers, they will establish a Bioinformatics RPM Repository on bioinformatics tools, the primary focus being NGS tools. The purpose is to come to a stable repository of easily installable packages for the common bioinformatics tools that can be used in (for example) Galaxy.

Be welcome to join our effort, which is just starting. Interested, please email hailiang dot mei at nbic dot nl or bits at vib.be.

Maintainers

Overview tools

Tool NGS pipeline part Link to RPM? Link to tool Priority? Maintainer
bfast Aligner Yes - [1] http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page
Bowtie Aligner No http://bowtie-bio.sourceforge.net/index.shtml BITS
BWA Aligner YES – [2] http://bio-bwa.sourceforge.net/
Cgatools Format conversion - Analysis:SNP detection No http://cgatools.sourceforge.net/ BITS
FastQC Quality control No http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/
Filo Format conversion No https://github.com/arq5x/filo/
HiTec Quality control No http://www.csd.uwo.ca/~ilie/HiTEC/
Maq Aligner YES – [3] http://maq.sourceforge.net
Mosaik-aligner Aligner No http://code.google.com/p/mosaik-aligner/
PASS Aligner No http://pass.cribi.unipd.it/cgi-bin/pass.pl?action=Download
Picard-tools Format conversion No http://picard.sourceforge.net/command-line-overview.shtml
Pindel Analysis: SV No https://trac.nbic.nl/pindel/ David van Enckevort
Samstat Quality control No http://samstat.sourceforge.net/ BITS
Samtools Format conversion YES – rpmsearch http://samtools.sourceforge.net/
Bamtools Format Conversion No http://sourceforge.net/projects/bamtools/
Bamview Visualisation No http://bamview.sourceforge.net/
Shrimp Aligner No http://compbio.cs.toronto.edu/shrimp/
SOAP Aligner No http://soap.genomics.org.cn/soapaligner.html
SOCS Aligner - Solid No http://solidsoftwaretools.com/gf/project/socs/
Tabix Format conversion No http://sourceforge.net/projects/samtools/files/
Vcftools Format conversion - Data mining No http://vcftools.sourceforge.net/
Genomeanalysis TK Quality control - Analysis No http://www.broadinstitute.org/gsa/wiki/index.php/Main_Page#The_Genome_Analysis_Toolkit_.28GATK.29
Fastxtoolkit Quality control No http://hannonlab.cshl.edu/fastx_toolkit/
pe-asm Assembling No http://code.google.com/p/pe-asm/
prinseq Quality control No http://prinseq.sourceforge.net
PerM Aligner No http://code.google.com/p/perm/
Kent Tools Format conversion No http://hgwdev.cse.ucsc.edu/~kent/
Bedtools Data mining YES – [4]
Repeatmasker Cleaning No http://www.repeatmasker.org/

Additional links to NGS tools

Additional Linux package repositories for bioinformatics tools

.deb