Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

By Heng Li. Bioinform., 2015

1,394 citations recorded by the source corpus.

MOTIVATION Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10 kb in length, which have enabled high-quality genome assembly at an affordable cost. However, at present, long reads have an error rate as high as 10-15%. Complex and computationally intensive pipelines are required to assemble such reads. RESULTS We present a new mapper, minimap and a de novo assembler, miniasm, for efficiently mapping and assembling SMRT and ONT reads without an error correction stage. They can often assemble a sequencing run of bacterial data into a single contig in a few minutes, and assemble 45-fold Caenorhabditis elegans data in 9 min, orders of magnitude faster than the existing pipelines, though the consensus sequence error rate is as high as raw reads. We also introduce a pairwise read mapping format and a graphical fragment assembly format, and demonstrate the interoperability between ours and current tools. AVAILABILITY AND IMPLEMENTATION https://github.com/lh3/minimap and https://github.com/lh3/miniasm CONTACT hengli@broadinstitute.org SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

Subfields: Ecology, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/676fe85da757abb8320a527efc737543f78ddafa

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Citations in the corpus

Integrating Hi-C links with assembly graphs for chromosome-scale assembly (2018, background): “SALSA2 requires the unitig sequences and, optionally, a GFA-format graph (Li, 2016) representing the ambiguous reconstructions.”
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads (2020, methodology): “The D. melanogaster HiFi data are available from NCBI BioProject database (https://www.ncbi.nlm.nih.gov/bioproject/) at PRJNA573706 (SRR10238607; median: 24.4 kbp; mean: 24.4 kbp) and CLR (SRR9969843; median 13.3 kbp; mean: 17.2 kbp).”
ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads (2017, methodology): “Reads are mapped to the reference sequences using minimap [17] to produce a set of reads for each cluster.”
Protein-to-genome alignment with miniprot (2022, background): “Let B = ψ(φ(P )) where ψ(·) is an invertible integer hash function (Li, 2016) over [0, 2).”
Oxford Nanopore MinION Sequencing and Genome Assembly (2016, methodology): “Miniasm is the fastest assembler examined in this paper, taking only a few minutes for a bacterial-sized genome.”
Significantly improving the quality of genome assemblies through curation (2020, neutral): “long reads Minimap2 [43] , winnowmap [44] x x x x”
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads (2016, methodology): “Miniasm is a longread-only assembler which, unlike HGAP and Canu, does not produce a consensus sequence [48].”
A complete Cannabis chromosome assembly and adaptive admixture for elevated cannabidiol (CBD) content (2018, methodology): “Genotypes were updated via imputation using a sliding-window hidden markov model using LB-Impute (23) leveraging variant coverage information 35 and physical linkage within a window of width 10 variants.”
Nanopore sequencing technology, bioinformatics and applications (2021, background): “…Flye improves genome assembly at long and highly repetitive regions by constructing an assembly graph from concatenated disjoint genomic segments 110 ; Miniasm uses all-versus-all read self-mapping for ultrafast assembly 107 , although postassembly polishing is necessary for higher accuracy.”