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| Software | Description |
|---|---|
| build-essential | gcc, g++, make, cmake, patch, autoconf, automake, m4, bison, libtool |
| emacs, vi, vim, ed | text editors |
| postfix | mail programs |
| perl | perl interpretor |
| python 2 | python version 2 interpretor |
| python 3 | python version 3 interpretor |
| ruby | ruby programming language |
| samba | Windows SMB/CIFS file and printer sharing protocol and applications |
| screen, tmux | Text window managers (multiplexer) |
| ssh | Secure Shell (remote access) |
| sudo | Root access for POD delegates only |
| tar | File archiving utility |
| wget, curl | Remote file/url transfer utilities |
| gzip, zip, unzip | File compression and archiving tools. |
Standard BioLinux Packages
| Software | Version | Description |
|---|---|---|
2.0.2-3 | de novo, parallel, sequence assembler for short reads | |
bamtools | 2.4.1+dfsg-2 | toolkit for manipulating BAM (genome alignment) files |
bedtools | 2.26.0+dfsg-5 | suite of utilities for comparing genomic features |
| bioperl | 1.7.2-2 | Perl tools for computational molecular biology |
bioperl-run | 1.7.1-3 | BioPerl wrappers: scripts |
| blast2 | 1:2.6.0-1 | Basic Local Alignment Search Tool |
| bowtie | 1.2.2+dfsg-2 | Ultrafast memory-efficient short read aligner |
| bowtie2 | 2.3.4.1-1 | Ultrafast memory-efficient short read aligner |
| bwa | 0.7.17-1 | Burrows-Wheeler Aligner |
| cd-hit | 4.6.8-1 | a suite of programs designed to quickly group sequences |
clustalw | 2.1+lgpl-5 | No description |
clustalx | 2.1+lgpl-6 | No description |
cufflinks | 2.2.1+dfsg.1-2 | Transcript assembly, differential expression and regulation for RNA-Seq |
ea-utils | 1.1.2+dfsg-4build1 | command-line tools for processing biological sequencing data |
emboss | 6.6.0+dfsg-6build1 | european molecular biology open software suite |
emboss-lib | 6.6.0+dfsg-6build1 | EMBOSS Libraries |
fastqc | 0.11.5+dfsg-6 | A quality control application for high throughput sequence data |
fastx-toolkit | 0.0.14-5 | FASTQ/A short nucleotide reads pre-processing tools |
hmmer | 3.1b2+dfsg-5ubuntu1 | profile hidden Markov models for protein sequence analysis |
jaligner | 1.0+dfsg-4 | Smith-Waterman algorithm with Gotoh’s improvement |
jellyfish | 2.2.8-3build1 | count k-mers in DNA sequences |
khmer | 2.1.2+dfsg-3 | k-mer counting, filtering and graph traversal |
libbiojava-java | 1:1.7.1-7 | Java API to biological data and applications (default version) |
libbiojava-java-demos | 1:1.7.1-7 | Example programs for BioJava |
macs | 2.1.1.20160309-2 | Model-based Analysis of ChIP-Seq on short reads sequencers |
mafft | 7.310-1 | Multiple alignment program for amino acid or nucleotide sequences |
maq | 0.7.1-7 | maps short fixed-length polymorphic DNA sequence reads to reference sequences |
Standard Third-Party Software
| Software | Description |
|---|---|
| R, Rscript | R command-line shell and script execution programs. |
| Matlab | MathWorks Matlab Software. See How do I use MATLAB on the POD? |
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