Biology Research Works
Permanent URI for this collectionhttp://hdl.handle.net/1903/13
Browse
2 results
Search Results
Item Genome assembly forensics: finding the elusive mis-assembly(Springer Nature, 2008-03-14) Phillippy, Adam M; Schatz, Michael C; Pop, MihaiWe present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation pipeline, called amosvalidate. We demonstrate the application of our pipeline in both bacterial and eukaryotic genome assemblies, and highlight several assembly errors in both draft and finished genomes. The software described is compatible with common assembly formats and is released, open-source, at http://amos.sourceforge.net .Item Searching for SNPs with cloud computing(Springer Nature, 2009-11-20) Langmead, Ben; Schatz, Michael C; Lin, Jimmy; Pop, Mihai; Salzberg, Steven LAs DNA sequencing outpaces improvements in computer speed, there is a critical need to accelerate tasks like alignment and SNP calling. Crossbow is a cloud-computing software tool that combines the aligner Bowtie and the SNP caller SOAPsnp. Executing in parallel using Hadoop, Crossbow analyzes data comprising 38-fold coverage of the human genome in three hours using a 320-CPU cluster rented from a cloud computing service for about $85. Crossbow is available from http://bowtie-bio.sourceforge.net/crossbow/ .