Details

Autor(en) / Beteiligte

• Simpson, Jared T
• Wong, Kim
• Jackman, Shaun D
• Schein, Jacqueline E
• Jones, Steven J M
• Birol, Inanç

Titel

ABySS: a parallel assembler for short read sequence data

Ist Teil von

• Genome Research, 2009-06, Vol.19 (6), p.1117-1123

Ort / Verlag

United States: Cold Spring Harbor Laboratory Press

Erscheinungsjahr

2009

Link zum Volltext

Quelle

MEDLINE

Beschreibungen/Notizen

• Widespread adoption of massively parallel deoxyribonucleic acid (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 > or =100 base pairs (bp) in length were created with an N50 size of 1499 bp, 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.