ABySS 2.0: Resource-Efficient Assembly of Large Genomes using a Bloom Filter

Abstract

The assembly of DNA sequences de novo is fundamental to genomics research. It is the first of many steps towards elucidating and characterizing whole genomes. Downstream applications, including analysis of genomic variation between species, between or within individuals critically depends 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 messagepassing system (MPI). We present here its re-design, 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 present assembly benchmarks of human Genome in a Bottle 250 bp Illumina paired-end and 6 kbp mate-pair libraries from a single individual, yielding a NG50 (NGA50) scaffold contiguity of 3.5 (3.0) Mbp using less than 35 GB of RAM, a modest memory requirement by today's standard that 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 contiguity of this assembly to 42 (15) Mbp.

ARCS: Assembly Roundup by Chromium Scaffolding

“…Both pairedend and mate-pair reads were corrected with BFC v181 [12] (with the parameter -s3G). Contigs and scaffolds were assembled with ABySS v2.0 [9] with the command: abyss-pe name=hsapiens np=64 k=144 q=15 v=-v l=40 s=1000 n=10 S=1000-10000 N=7 mp6k de=-mean mp6k n=1 lib=pe400 mp=mp6k, where pe400 and mp6k are variables listing all files containing paired-end sequencing and MPET reads, respectively.…”

“…For the genome assembly contig and scaffold baselines, we first downloaded Illumina whole genome shotgun (WGS) 2x250 bp paired-end sequencing data and Illumina 6 kbp mate-pair data for an Ashkenazi female (NA24143). ABySS-2.0 [9] was used to assemble the whole-genome shotgun paired-end and mate-pair reads into contigs and scaffolds and Chromium reads were aligned to those sequences. Using these alignments as input, we ran and benchmarked ARCS (v1.0.0), Architect (v0.1) and fragScaff (v140324) to further scaffold contig and scaffold baseline sequences 3 kbp and longer, as recommended [4], while investigating the effects of multiple parameter combinations on scaffolding (Table S1), reporting contiguity length metrics and breakpoints from sequence alignments to the reference human genome, which serves as a proxy for counting large-scale misassemblies in both contigs and scaffolds.…”

“…Breakpoints (x 1,000) To assess correctness, we aligned the assemblies to the primary chromosome sequences of the human reference GRCh38 and counted the number of observed breakpoints using abyss-samtobreak [9]. At the contig level ( Fig.…”

Chromium Sequencing: The Doors Open for Genomics of Obligate Plant Pathogens

“…Trimmomatic v 0.36 [24] and NxTrim v 0.4.2 [25] were used with the default options to trim paired-end and mate-pair reads. We used ABySS 2.0 [26] to assemble (k-mer99) paired-end reads, and to scaffold with mate-pair reads. Only scaffolds 500bp were retained.…”

Overlap graphs and de Bruijn graphs: data structures for de novogenome assembly in the big data era

“…ABySS 2.0. ABySS 2.0 [44], just as with Minia, uses a Bloom filter representation of the de Bruijn graph. Its innovative unitig assembly stage, which is performed on the Bloom filter, allows to reduce the memory requirements by an order of magnitude, while maintaining results comparable with existing assemblers.…”