This is the Linux app named iCAS - An Illumina Clone Assembly System to run in Linux online whose latest release can be downloaded as icas_v062.tar.bz2. It can be run online in the free hosting provider OnWorks for workstations.
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iCAS - An Illumina Clone Assembly System to run in Linux online
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.
This is an application that can also be fetched from https://sourceforge.net/projects/icas/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.