ABySS: A parallel assembler for short read sequence data

TLDR

Massively parallel DNA sequencing has spurred the development of de novo short‑read assemblers, yet existing tools cannot efficiently assemble the vast data from large‑scale projects such as whole‑human‑genome sequencing. The authors developed ABySS, a parallelized assembler, to overcome this inefficiency. ABySS employs parallel computing to assemble large short‑read datasets, as demonstrated by assembling 3.5 billion paired‑end reads from an African male genome released by Illumina. The assembly produced 2.76 million contigs ≥100 bp with an N50 of 1499 bp, covering 68 % of the reference genome, and revealed polymorphic and novel sequences validated against alternate human and primate assemblies.

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 ( A ssembly By S hort S equences), 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 ≥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.