Lubuntu_14.04_Bioinformatics_v0.6

Update March 2016

This update of the ISO file is based on the same (14.04) version of Lubuntu, but includes additional software tools in addition to those present in the v0.5 release. The SHA1 checksum for the new version is 293c2acdbe0494ca3bedfb3244a30c882db744bb

New software packages include:

BWA v0.7.12-r1044

• Heng Li's Burrows-Wheeler alignment package, with settings for aligning PacBio and Oxford Nanopore 2D long single-molecule reads.

Samtools v1.3 and BCFtools v1.3

• the HTSlib-enabled versions of samtools and bcftools for managing and manipulating files of alignments and variant calls.

GBSX

• a package for simulating results of single-digest or double-digest restriction-enzyme-based reduced representation sequencing from a reference genome sequence.

BEDtools2

• a package for manipulating and managing BED files; tab-delimited text files that specify genomic regions and can be used to direct the focus of, or document results of, analysis of sequence files.

BBTools

• Brian Bushnell's Java toolkit for sequence trimming, filtering, sorting, and alignment (among other functions).

Lubuntu 14.04 live USB for DNA sequence analysis

Analytical and General Tools

• R v3.1, with lattice, RSQLite, and matrix packages
• Bioconductor, with GenomicFeatures, biomaRt, GenomicRanges, Rsamtools, rtracklayer, DESeq2
• Open JDK 7
• bwa 0.7.10
• samtools 0.1.19, with razip, bcftools, and vcfutils.pl
• fastx-toolkit
• GemSIM v 1.6 DNA sequence read simulator and associated Python programs
• SciTE editor
• extundelete

Libraries and System Tools

• tcl-tk 8.5
• Gnu Scientific Libraries
• Google sparsehash
• scintilla
• Python with python-scipy, python-numpy, and python-nose