MOTIVATION: The de novo assembly of short read high-throughput sequencing data poses significant computational challenges. The volume of data is huge; the reads are tiny compared to the underlying sequence, and there are significant numbers of sequencing errors. There are numerous software packages that allow users to assemble short reads, but most are either limited to relatively small genomes (e.g. bacteria) or require large computing infrastructure or employ greedy algorithms and thus often do not yield high-quality results. RESULTS: We have developed Gossamer, an implementation of the de Bruijn approach to assembly that requires close to the theoretical minimum of memory, but still allows efficient processing. Our results show that it is space efficient and produces high-quality assemblies. AVAILABILITY: Gossamer is available for non-commercial use from http://www.genomics.csse.unimelb.edu.au/product-gossamer.php.
MOTIVATION: The de novo assembly of short read high-throughput sequencing data poses significant computational challenges. The volume of data is huge; the reads are tiny compared to the underlying sequence, and there are significant numbers of sequencing errors. There are numerous software packages that allow users to assemble short reads, but most are either limited to relatively small genomes (e.g. bacteria) or require large computing infrastructure or employ greedy algorithms and thus often do not yield high-quality results. RESULTS: We have developed Gossamer, an implementation of the de Bruijn approach to assembly that requires close to the theoretical minimum of memory, but still allows efficient processing. Our results show that it is space efficient and produces high-quality assemblies. AVAILABILITY: Gossamer is available for non-commercial use from http://www.genomics.csse.unimelb.edu.au/product-gossamer.php.
Authors: Gordon M Daly; Richard M Leggett; William Rowe; Samuel Stubbs; Maxim Wilkinson; Ricardo H Ramirez-Gonzalez; Mario Caccamo; William Bernal; Jonathan L Heeney Journal: PLoS One Date: 2015-06-22 Impact factor: 3.240
Authors: Marcus Lefebure; Richard W Tothill; Elizabeth Kruse; Edwin D Hawkins; Jake Shortt; Geoffrey M Matthews; Gareth P Gregory; Benjamin P Martin; Madison J Kelly; Izabela Todorovski; Maria A Doyle; Richard Lupat; Jason Li; Jan Schroeder; Meaghan Wall; Stuart Craig; Gretchen Poortinga; Don Cameron; Megan Bywater; Lev Kats; Micah D Gearhart; Vivian J Bardwell; Ross A Dickins; Ross D Hannan; Anthony T Papenfuss; Ricky W Johnstone Journal: Nat Commun Date: 2017-03-06 Impact factor: 14.919