Personal tools
You are here: Home / HowTo / Compute Cluster / Software

Installed software

List of software installed on user requests
name description version installation source
install location/nodes
R

language and environment for statistical computing and graphic

2.7.2

2.10.1

source code /usr/local
/usr/local/R-2.10.1
bioConductor

R library for analysis and comprehension of genomic data

2.2

source code

/usr/local
bioruby

Ruby library for bioinformatics

1.2.1

source code

/usr/local
boost multi-purpose C libraries 1.33.1 SLES package
graphviz graph vizualisation programs 2.20 source code /usr/local
meme motif search programs 4.0 source code /usr/local
GAPipeline GenomeAnalyzer pipeline for Solexa 1.3.2 source code /usr/local/GAPipeline-x.x.x
1.3.4
1.4.0
CASAVA
Consensus Assessment of Sequence and Variation 1.6
source code
/usr/local/CASACA1.6.0
OLB
Illumina Offline Base Caller
1.6.0
1.8.0
1.9.0
source code
/usr/local/OLB-1.6-0
/usr/local/OLB-1.8.0
/usr/local/OLB-1.9.0
APT Affymetrix power tools 1.10.2 source code /usr/local/affymetrix_power_tools/
BirdSuite

tools to detect and report SNP genotype, CNV etc.

1.5.3 source code + MatLab compiled runtime /usr/local/birdsuite
maq Mapping and Assembly with Qualities 0.7.1 source code /usr/local
samtools
tools for the Sequence Alignment/Map format
0.1.8r3
source code
/usr/local
bowtie
ultrafast, memory-efficient short read aligner 0.12.5
source code
/usr/local/bowtie
tophat
fast splice junction mapper for RNA-Seq reads 1.0.14
source code
/usr/local
cufflinks
Transcript assembly, differential expression, and differential regulation for RNA-Seq
0.8.3
source code
/usr/local


1.0.2
source code /usr/local
bwa
Burrows-Wheeler Aligner 0.5.8a
source code
/usr/local
octave
high-level language, primarily intended for numerical computations 3.2.3
source code
/usr/local
shogun-toolbox
Large Scale Machine Learning Toolbox
0.9.0
source code
/usr/local
seqan library and tools
C++ library of efficient algorithms and data structures for the analysis of sequences 1.2
source code
/usr/local
ncbi blast
NCBI blast

source code
/usr/local
mpiblast
parallel version of blast
1.4
source code
/usr/local
possumsearch
search for position specific scoring matrice 1.3
source code
/usr/local
hmmer3
hidden Markov model based search
3.0b3 source code
/usr/local
bedtools
tools for working with BED files
2.5.1
source code
/usr/local
wtap
Solid Whole Transcriptome Analysis Pipeline
1.2.1
source code
/usr/local/ab_wtp_v1.2.1/  See
splitseek.pl
de novo prediction of splice junctions in RNA-seq 1.3.2
source code
/usr/local
fastx toolkit
collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing 0.0.13
source code
/usr/local
google sparsehash A memory-efficient hash_map implementation, see details  1.7 source code /usr/local
Document Actions