ABySS

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.

ABySS: a parallel assembler for short read sequence data.

ABySS is a tool for de novo genome assembly using short read data. It implements a distributed representation of de Bruijn graphs, which enable parallel computation of the assembly algorithm.  ABySS stands for Assembly By Short Sequencing.

ABySS

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