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Odyssey Software Updates, June-2015

Software updates and installs since May 1st:

NOTE: All software is installed under the Lmod module system on Odyssey. And please read our guidelines for software install requests.

armadillo 5.100.2 Fast C++ matrix library with easy to use functions and syntax, deliberately similar to Matlab
ART 031915 Simulation tools to generate synthetic next-generation sequencing reads
bcftools 1.2 Set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF
BEAST 1.8.2 Bayesian Evolutionary Analysis by Sampling Trees
BEAST 2.1.3 Bayesian Evolutionary Analysis by Sampling Trees
bismark 0.14.2 Bisulfate read mapper and methylation caller
clustalo 1.2.0 Multiple sequence alignment
cutadapt 1.8.1 Trims adapter sequence from fastq files
emboss 6.6.0 EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community
FragGeneScan 1.19 Application for finding (fragmented) genes in short reads.
GenomeAnalysisTK 3.3.0 Genome Analysis ToolKit version 3.3.0
libmesh 0.9.4 Framework for numerical simulation of partial differential equations
MaxBin 1.4.5 An automatic tool for binning metagenomics sequences
netcdf 4.3.2 Libraries for array-oriented scientific data format
oommf 1.2a5bis Object Oriented MicroMagnetic Framework
OpenBLAS 0.2.14 Open source linear algebra library
petsc 3.5.4 Portable extensible toolkit for scientific computation
samtools 1.2 Utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
slepc 3.5.4 Scalable library for eigenvalue problem computations
SPAdes 3.5.0 St. Petersburg genome assembler for both standard isolates and single cell MDA bacteria
SweeD 3.3.2 Composite likelihood ratio test for detecting selective sweeps
tcl 8.6.4 Dynamic programming language, suitable for a very wide range of uses
tk 8.6.4 Open source, cross-platforM widget toolkit
trinityrnaseq 2.0.6 De novo assembler from RNA Seq from Broad Inst. et al.
trinityrnaseq r20140717 De novo assembler from RNA Seq from Broad Inst. et al.
vapor 2.4.0 Visualization and Analysis Platform for Ocean, Atmosphere, and Solar Researchers
VarScan 2.3.7 Variant detection in massively parallel sequencing data
visit 2.9.1 Open Source, interactive, scalable, visualization, animation and analysis tool

Last updated: June 23, 2015 at 8:22 am

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