iAssembler

iAssembler assembles Expressed Sequence Tags (ESTs) into accurate consensus sequences to improve de novo transcriptome assemblies for organisms lacking reference genomes.

Key Features:

• Integration of established assemblers: Uses MIRA and CAP3 to generate initial contig assemblies from large-scale EST datasets for preliminary sequence alignment and merging.
• Error correction mechanisms: Identifies and corrects two common EST assembly errors: chimeric contigs that merge ESTs from different transcripts (including alternatively spliced variants or paralogs) and fragmented assemblies where ESTs from the same transcript fail to assemble together.
• Sequencing technology compatibility: Processes EST data generated by Sanger sequencing and Roche-454 massive parallel pyrosequencing.
• Benchmarking and performance: Has been compared with other de novo EST assembly programs using Roche-454 and Sanger datasets and demonstrated superior consensus-sequence accuracy.

Scientific Applications:

• Gene discovery: Produces accurate consensus sequences to support discovery of coding transcripts in non-model organisms.
• Functional analysis: Provides higher-quality consensus sequences for downstream functional characterization of genes.
• Gene annotation: Improves reliability of gene annotation by reducing assembly-induced errors in EST-derived consensus sequences.
• Expression profiling: Enables more reliable expression profiling by supplying corrected consensus sequences for transcript quantification.
• Comparative genomics: Facilitates comparative analyses by generating reliable transcript sequences for cross-species comparisons.

Methodology:

The pipeline first uses MIRA and CAP3 to create initial assemblies from EST datasets and then applies an error-correction process to identify and rectify chimeric and fragmented transcriptome assembly errors.