mrsFast: a cache-oblivious algorithm for short-read mapping

By Faraz Hach, Fereydoun Hormozdiari, Can Alkan, Farhad Hormozdiari, Inanç Birol, Evan E. Eichler, Süleyman Cenk Sahinalp. Nature Methods, 2010

314 citations recorded by the source corpus.

In addition to single-nucleotide variations and small insertions-deletions (indels), largersized structural variations (for example, insertions, deletions, inversions, segmental duplications and copy-number polymorphisms) contribute to human genetic diversity. In almost all recent structural variation discovery (SVD) studies, short reads from a donor genome have been mapped to a reference genome as a first step. The accuracy of such an SVD study is directly correlated to the accuracy of this mapping step, which also provides the main computational bottleneck of the SVD study.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/6e5b65a99d484bc623ac4f8c9d911fad6065945b

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In Genetics

1. Aaron R. Quinlan
2. Erik P. Garrison
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6. Evan E. Eichler
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In Molecular Biology

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2. Alicia Oshlack
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In Plant Science

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4. Aaron R. Quinlan
5. Alicia Oshlack
6. John C. Marioni

Citations in the corpus

• Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. (2012, unknown): “Assembly The currently accepted methods most capable of assembling NGS data utilize Kmer DeBruijn graph traversalbased methods, including programs such as Velvet, SOAPdenovo, ALLPATHS, ABySS, the CLC Bio commercial www.sciencedirect.com product as well as number of newer assemblers under development”
• From RNA-seq reads to differential expression results (2010, methodology): “Current aligners enable fast heuristic matching by using either hash tables [19-22] or the Burrows Wheeler transform (BWT) [23-25].”
• Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives (2013, methodology): “It utilizes mrsFAST to map reads, allowing up to 2 mismatches [43].”
• Tools for mapping high-throughput sequencing data (2012, background): “Li and Homer (2010) showed that gapped alignment increases the percentage of reads mapped but that it did not reduce the percentage of reads incorrectly aligned.”
• MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping (2013, background): “Competing Interests: The authors have declared that no competing interests exist.”
• Copy number variation detection and genotyping from exome sequence data (2012, methodology): “the repeat-masked hg19 reference sequence using mrsFAST (Hach et al. 2010), allowing for up to two mismatches per 36 bp.”