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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


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 (