Computer Science Research Works

Permanent URI for this collectionhttp://hdl.handle.net/1903/1593

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    Genome assembly forensics: finding the elusive mis-assembly
    (Springer Nature, 2008-03-14) Phillippy, Adam M; Schatz, Michael C; Pop, Mihai
    We 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 .
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    Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    (Springer Nature, 2009-03-04) Langmead, Ben; Trapnell, Cole; Pop, Mihai; Salzberg, Steven L
    Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source http://bowtie.cbcb.umd.edu .