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Related Articles ABySS: A parallel assembler for short read sequence data.
Genome Res. 2009 Feb 27;
Authors: Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I
Widespread adoption of massively parallel DNA sequencing instruments has prompted the recent development of de novo short read assembly algorithms. A common shortcoming of the available tools is their inability to efficiently assemble vast amounts of data generated from large-scale sequencing projects, such as the sequencing of individual human genomes to catalog natural genetic variation. To address this limitation, we developed ABySS (Assembly By Short Sequences), a parallelized sequence assembler. As a demonstration of the capability of our software, we assembled 3.5 billion paired-end reads from the genome of an African male publicly released by Illumina Inc. Approximately 2.76 million contigs >/=100bp in length were created with an N50 size of 1499bp, representing 68% of the reference human genome. Analysis of these contigs identified polymorphic and novel sequences not present in the human reference assembly, which were validated by alignment to alternate human assemblies and to other primate genomes.
PMID: 19251739 [PubMed - as supplied by publisher]
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Related Articles ABySS: A parallel assembler for short read sequence data.
Genome Res. 2009 Feb 27;
Authors: Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I
Widespread adoption of massively parallel DNA sequencing instruments has prompted the recent development of de novo short read assembly algorithms. A common shortcoming of the available tools is their inability to efficiently assemble vast amounts of data generated from large-scale sequencing projects, such as the sequencing of individual human genomes to catalog natural genetic variation. To address this limitation, we developed ABySS (Assembly By Short Sequences), a parallelized sequence assembler. As a demonstration of the capability of our software, we assembled 3.5 billion paired-end reads from the genome of an African male publicly released by Illumina Inc. Approximately 2.76 million contigs >/=100bp in length were created with an N50 size of 1499bp, representing 68% of the reference human genome. Analysis of these contigs identified polymorphic and novel sequences not present in the human reference assembly, which were validated by alignment to alternate human assemblies and to other primate genomes.
PMID: 19251739 [PubMed - as supplied by publisher]
More...