Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

By Konstantin Berlin, Sergey Koren, Chen-Shan Chin, James P Drake, J. Landolin, Adam M. Phillippy. Nature Biotechnology, 2014

901 citations recorded by the source corpus.

Long-read, single-molecule real-time (SMRT) sequencing is routinely used to finish microbial genomes, but available assembly methods have not scaled well to larger genomes. We introduce the MinHash Alignment Process (MHAP) for overlapping noisy, long reads using probabilistic, locality-sensitive hashing. Integrating MHAP with the Celera Assembler enabled reference-grade de novo assemblies of Saccharomyces cerevisiae, Arabidopsis thaliana, Drosophila melanogaster and a human hydatidiform mole cell line (CHM1) from SMRT sequencing. The resulting assemblies are highly continuous, include fully resolved chromosome arms and close persistent gaps in these reference genomes. Our assembly of D. melanogaster revealed previously unknown heterochromatic and telomeric transition sequences, and we assembled low-complexity sequences from CHM1 that fill gaps in the human GRCh38 reference. Using MHAP and the Celera Assembler, single-molecule sequencing can produce de novo near-complete eukaryotic assemblies that are 99.99% accurate when compared with available reference genomes.

Subfields: Ecology, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/618d82a202bb0408e388eba250c66c8a90700c81

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Citations in the corpus

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis (2017, methodology): “Several tools aim to reduce these error rates including LSC 31 , proovread 32 , LoRDEC 33 , and PBcR 34, 35 .”
PacBio Sequencing and Its Applications (2015, background): “Drosophila melanogaster PacBio PBcR, MHAP, Celera, Quiver 42 121 132 1060 CPU hours for genome assembly (593 improvement over BLASR); improved current reference of telomeres [31]”
Oxford Nanopore MinION Sequencing and Genome Assembly (2016, positive): “…signiﬁcant performance improvements in assembling bacterial genomes [43,44], middle-sized Drosophila melanogaster and Arabidopsis thaliana genomes [45], and more recently human genomes [46,47], thanks to the implementation of a new, faster algorithm called MinHash alignment process (MHAP) [45].”
Alignment-free sequence comparison: benefits, applications, and tools (2017, methodology): “Integration of the MinHash Alignment Process with the Celera Assembler enabled reference-grade de novo assemblies of several eukaryotic genomes [76].”
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation (2016, methodology): “2 (Berlin et al. 2015).”
Assembly of long error-prone reads using de Bruijn graphs (2016, methodology): “The pioneer in long reads technologies, Pacific Biosciences, now produces accurate assemblies from long error-prone reads (1, 2).”
Assembly of long, error-prone reads using repeat graphs (2018, methodology): “We ignored small connected components in the bacterial assembly graphs (which represent plasmids that do not share repeats with chromosomes) and classified an assembly as (1) complete if the assembly graph consists of a single loop-edge representing a circular chromosome, (2) semicomplete if the ass”
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences (2015, methodology): “Raw read overlap BLASR Chaisson and Tesler (2012) DALIGNER Myers (2014) MHAP Berlin et al. (2015) GraphMap Sovic et al. (2015) minimap this article Error correction pbdagcon http://bit.ly/pbdagcon falcon sense http://bit.ly/pbfcasm nanocorrect Loman et al. (2015) Assembly wgs-assembler Myers et al. ”
Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions (2016, positive): “Indeed, long reads from the Paci ﬁ c Biosciences Single Molecule, Real-Time (SMRT) platform currently produce highly connected de novo assemblies with low error rates (Berlin et al. 2015; English et al. 2015; Pendleton et al. 2015; VanBuren et al. 2015).”
The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies (2019, methodology): “One can either use it early in the process to correct long reads, as is done in the PBcR [2] and MaSuRCA [3] assemblers, or one can use it after the long read assembly has been completed to improve the quality of the consensus by aligning the Illumina reads to the assembly.”
Circlator: automated circularization of genome assemblies using long sequencing reads (2015, methodology): “We ran a de novo assembly of the reads using PBcR, in order to generate the contigs and corrected reads required as input to Circlator, using the data and instructions at [29] and checkout revision 4642 of the source code.”