The est2assembly platform is the only platform for standardising transcriptome projects: go from raw trace files to an annotated GBrowse interface driven by the Seqfeature database. It accepts both Sanger and 454 sequencing technology for a denovo assembly, annotation and data mining of EST data.
It is available from http://est2assembly.googlecode.com
The platform makes use of a number of BioPerl and other tools such as prot4EST. Depending on what you want to use it for, not all of these need to be installed. Please see the manual.
- Currently makes use of MIRA and Newbler cDNA assemblers (the only NGS assemblers currently designed for ESTs)
- Standardized methods for judging transcriptome quality
- In active development for more packages for transcriptome analysis (e.g. digital transcriptomics with edgeR, curation and others)
Demos and Screenshots
Screenshots are available from the project website.
This software is GPLv2+ licensed as part of the Drupal package. It is currently supported by Alexie Papanicolaou while at CSIRO, the Australian Commonwealth Scientific and Research Organization (http://www.csiro.au).