Sequence Assembly Software

STARS

STARS is an alternative interface to staden for sequence assembly for sequence typing projects. Sequence typing projects typically involve the sequencing of the same gene, or gene fragment, many times in order to determine polymorphisms. The standard staden interfaces, pregap4 and gap4,are more suited to assembling long contigs. The STARS interface, on the other hand has been designed with sequence typing projects in mind and allows the assembly of large numbers of short contigs into the same database. These contigs can be retrieved and edited from the interface using a standard staden contig editor. The system also performs user logging etc and can therefore be used as a lab database for your projects. The software was initially designed for managing sequencing projects using Multi Locus Sequence Typing (MLST) of bacteria. It is available free of charge under the General Public License. This software is for UNIX systems and you will first need to install Staden. STARS is written by Man-Suen Chan and Nicki Gray.

STARS website

CLC Main Workbench

CLC Main Workbench creates a software environment enabling users to make a large number of advanced DNA, RNA, and protein sequence analyses, combined with gene expression analysis and data management.

This is commercial software with a 30 day trial period.

The MLST module is able to download schemes from PubMLST.org, and other MLST websites, to streamline allele and profile assignment.

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Software useful for MLST

This page contains links to software that is useful for assembling MLST data.

Running STARS on Linux

STARS was originally written to run on Solaris, but can be made to run satisfactorily on Linux. Here are the steps that were required to install STARS on Bio-Linux. They may be useful for installing STARS on other Linux systems. Please contact Keith Jolley if you have any questions concerning the set-up or would like to obtain vector files suitable for automatic clipping for Neisseria or Campylobacter MLST systems. Further details about Bio-Linux can be found here.

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