RT Journal
A1 Jackman, Shaun D.
A1 Vandervalk, Benjamin P.
A1 Mohamadi, Hamid
A1 Chu, Justin
A1 Yeo, Sarah
A1 Hammond, S. Austin
A1 Jahesh, Golnaz
A1 Khan, Hamza
A1 Coombe, Lauren
A1 Warren, Rene L.
A1 Birol, Inanc
T1 ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter
JF Genome Research 
JO Genome Research 
YR 2017 
FD May 01 
VO 27 
IS 5 
SP 768 
OP 777 
DO 10.1101/gr.214346.116 
UL http://genome.cshlp.org/content/27/5/768.abstract 
AB The assembly of DNA sequences de novo is fundamental to genomics research. It is the first of many steps toward elucidating and characterizing whole genomes. Downstream applications, including analysis of genomic variation between species, between or within individuals critically depend on robustly assembled sequences. In the span of a single decade, the sequence throughput of leading DNA sequencing instruments has increased drastically, and coupled with established and planned large-scale, personalized medicine initiatives to sequence genomes in the thousands and even millions, the development of efficient, scalable and accurate bioinformatics tools for producing high-quality reference draft genomes is timely. With ABySS 1.0, we originally showed that assembling the human genome using short 50-bp sequencing reads was possible by aggregating the half terabyte of compute memory needed over several computers using a standardized message-passing system (MPI). We present here its redesign, which departs from MPI and instead implements algorithms that employ a Bloom filter, a probabilistic data structure, to represent a de Bruijn graph and reduce memory requirements. We benchmarked ABySS 2.0 human genome assembly using a Genome in a Bottle data set of 250-bp Illumina paired-end and 6-kbp mate-pair libraries from a single individual. Our assembly yielded a NG50 (NGA50) scaffold contiguity of 3.5 (3.0) Mbp using <35 GB of RAM. This is a modest memory requirement by today's standards and is often available on a single computer. We also investigate the use of BioNano Genomics and 10x Genomics’ Chromium data to further improve the scaffold NG50 (NGA50) of this assembly to 42 (15) Mbp.