ISMB/ECCB Stockholm 2009:
ISMB/ECCB
TT18: Arif Anwar - Analysis of next-generation genome and transcriptome re-sequencing data using integrated bioinformatics approaches and pipelines
June 29, 2009
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Synamatix; http://www.synamatix.com/
- Diego M. Riaño-Pachón
Established in 2001 by Robert Hercus
- Diego M. Riaño-Pachón
current challenges, managing data: storing and moving around
- Diego M. Riaño-Pachón
several steps in the analysis pipeline
- Diego M. Riaño-Pachón
open source software integrated into synamatix pipeline:one-stop bioinformatics service
- Diego M. Riaño-Pachón
de-novo genome and transcriptome assembly: no use of related genomes in the assembly process!
- Diego M. Riaño-Pachón
genome assembly:
- Diego M. Riaño-Pachón
Basic pipeline: remove contaminant; remove read artifacts, false PEs, homopolymers; trim poor quality reads
- Diego M. Riaño-Pachón
use rule matrix to filter and rank SNPs, indels, and structural variations
- Diego M. Riaño-Pachón
optimized algorithms for SNP detection even at low coverage
- Diego M. Riaño-Pachón
The use Circos (http://mkweb.bcgsc.ca/circos/) plots for visualization of CNAs and CNVs
- David G. Pisano
very fast comparative genomics of bacterial and eukaryotic genomes
- Diego M. Riaño-Pachón