title: ABySS: a parallel assembler for short read sequence data.
abstract: 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.
authors.affiliation: Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada.
authors.forename: Jared T
authors.initials: JT
authors.lastname: Simpson
authors.forename: Kim
authors.initials: K
authors.lastname: Wong
authors.forename: Shaun D
authors.initials: SD
authors.lastname: Jackman
authors.forename: Jacqueline E
authors.initials: JE
authors.lastname: Schein
authors.forename: Steven J M
authors.initials: SJ
authors.lastname: Jones
authors.forename: Inanç
authors.initials: I
authors.lastname: Birol
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D020451:Contig Mapping; D048168:Escherichia coli K12 / Q000235:genetics; D014644:Genetic Variation; D015894:Genome, Human; D006801:Humans; D011110:Polymorphism, Genetic; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software