est2assembly

est2assembly performs hybrid de novo transcriptome assembly and annotation by integrating Sanger and 454 pyrosequencing reads into annotated, GMOD-compatible EST resources.

Key Features:

• Hybrid de-novo assembly: Processes raw Sanger and 454 pyrosequencing reads into a combined hybrid de novo assembly.
• Annotation and data mining: Annotates assembled sequences and produces outputs compatible with GMOD, including generation of a SeqFeature database for GBrowse visualization.
• Assembler parameterization: Allows parameterization of assembler variables to tailor assembly configurations.
• Assembly quality assessment: Provides tools for assessing assembly quality to identify optimal assembly configurations.
• Support for EST datasets and non-model species: Targets large-scale EST datasets and transcriptome projects in non-model species.
• Shallow 454 sequencing support: Demonstrates that shallow 454 pyrosequencing datasets can yield useful transcriptome assemblies.

Scientific Applications:

• Processing public EST datasets: Processing public Sanger EST datasets from species such as Drosophila and Bicyclus.
• Sequencing technology comparison: Comparing Sanger and published 454 datasets to inform EST project design.
• Insect transcriptome assembly: Assembling and annotating new insect transcriptome collections.

Methodology:

Semi-automated processing of raw sequence data, hybrid de novo assembly, sequence annotation, assembler parameterization, and generation of GMOD-compatible outputs (SeqFeature database for GBrowse).