The problem refers to reconstructing the chromosome sequence(s) for a genome from sequencing reads, which are orders of magnitude shorter than the target genome ( Nagarajan and Pop 2013). 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.ĭe novo genome assembly remains a challenging problem, especially for large and complex genomes. This is a modest memory requirement by today's standards and is often available on a single computer. Our assembly yielded a NG50 (NGA50) scaffold contiguity of 3.5 (3.0) Mbp using <35 GB of RAM. 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. 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. 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). 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. Downstream applications, including analysis of genomic variation between species, between or within individuals critically depend on robustly assembled sequences. It is the first of many steps toward elucidating and characterizing whole genomes. The assembly of DNA sequences de novo is fundamental to genomics research.
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