Nextgen sequence tools

Info and links to documentation about tools on Bio-Linux for handling new sequencing data types

Next generation sequence data handling

Most software for handling and analysis of next generation sequencing data (454, Illumina, etc) can be installed on any Linux system. Software packages make this task easy. Dedicated Bio-Linux packages for this are listed below, along with packages we mirror from Debian that are maintained by Debian-Med. For a more extensive list of available software for handling data from the new sequencing technologies, try this listing on the seqanswers site, or this listing in the seqanswers forum.

Installing packages on Bio-Linux
Package names and descriptions
Utility scripts
Useful links
Next generation usergroups and mailing lists

Installing packages on Bio-Linux

Apart from the bio-linux-consed package, all packages listed below can be installed on a Bio-Linux system by typing

sudo apt-get update


sudo apt-get install packagename

The files installed by each of these packages can be listed using the command

dpkg -L packagename

Details of how to obtain and install the bio-linux-consed package can be found on our Bioinformatics FAQ page.

Package names and descriptions

bio-linux-assembly-conversion-tools Provides caftools, gap2caf, and roche2gap scripts for converting 454 assemblies into a format that can be opened by the assemby viewer/editor gap4. Pre-installed on Bio-Linux 6

bio-linux-consed Licensed software that can be used to view and edit Sanger, 454 or Solexa assemblies. Referenced-based alignments can be carried out using cross_match. See the Bio-Linux Bioinformatics FAQ for information on how to get access to this package for Bio-Linux.
bio-linux-mira Provides the mira assembly software. Pre-installed on Bio-Linux 6
bio-linux-mira-3rd-party Provides third party scripts available from the mira website. This includes two scripts for converting 454 paired end reads into CAF format, a script for binning tagged sequences and stripping off the tag, for converting lucy output to xml, and a script for extracting data from sff files with options for altering clip points. Pre-installed on Bio-Linux 6
maq Provides the maq software, along with utility scripts allowing many format conversions. Pre-installed on Bio-Linux 6
bio-linux-samtools Provides tools for working with nucleotide alignments in the binary BAM format (such as is produced using Bowie.) A partial tutorial for samtools. Pre-installed on Bio-Linux 6
ssake Provides the ssake software for assembling short sequences. Pre-installed on Bio-Linux 6
velvet Provides the velvet software, along with many contributed scripts that could useful to Velvet users. Pre-installed on Bio-Linux 6