iCAS - An Illumina Clone Assembly System

An Illumina clone assembly system using SOAPdenovo and ABySS

1 Download (This Week)
Last Update:
Download icas_v062.tar.bz2
Browse All Files

Description

Clone-by-clone sequencing, as a means of achieving high quality assemblies for large and complex genomes, continues to be of great relevance in the era of high throughput sequencing. However, assemblies obtained using current whole genome assemblers are often fragmented and sometimes have issues of genome completeness owing to different data characteristics introduced by multiplexed sequencing.

With iCAS the data filtering process is based on a novel kmer frequency algorithm, resulting in near perfect pre-assembly reads. Contigs are generated using different assembly algorithms and then merged together to achieve longer continuity. Re-aligning all the reads back to the draft contigs and recalibrating each sequence base achieves a final consensus. Using finished clones for QC, the pipeline is able to obtain assemblies with clone coverage of 99.7% and consensus base quality of Q39.

Developed at the Wellcome Trust Sanger Institute.

iCAS - An Illumina Clone Assembly System Web Site

KEEP ME UPDATED

Additional Project Details

Intended Audience

Science/Research

Programming Language

Perl, C

Registered

2014-07-14

Icons must be PNG, GIF, or JPEG and less than 1 MiB in size. They will be displayed as 48x48 images.