The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
Open accessAbstract
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Self-citation<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
Schleimer, S., S, W. D., & Aiken, A. (2003) · Proceedings of the 2003 ACM SIGMOD International Conference on Management of Data · doi:10.1145/872757.872770 · Cited by 1,099
Reducing storage requirements for biological sequence comparison
Roberts, M., Hayes, W., Hunt, B. R., Mount, S. M., & Yorke, J. A. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth408 · Cited by 485 · cited 2×
“Roberts et al. (2004) did not discuss the treatment of such equally good minimizers.”
BackgroundMethod
Cited by
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
Kim, D., Paggi, J. M., Park, C., Bennett, C., & Salzberg, S. L. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0201-4 · Cited by 15,022
Minimap2: Pairwise alignment for nucleotide sequences
Li, H. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty191 · Cited by 14,807
Self-citationHaplotype-resolved de novo assembly using phased assembly graphs with hifiasm
Cheng, H., Concepcion, G. T., Feng, X., Zhang, H., & Li, H. (2021) · Nature Methods · doi:10.1038/s41592-020-01056-5 · Cited by 5,859
Self-citationAssembly of long, error-prone reads using repeat graphs
Kolmogorov, M., Yuan, J., Lin, Y., & Pevzner, P. A. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0072-8 · Cited by 5,986
The complete sequence of a human genome
Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., Vollger, M. R., Altemose, N., Uralsky, L., Gershman, A., et al. (2022) · Science · doi:10.1126/science.abj6987 · Cited by 3,136
Self-citationNanopore sequencing and assembly of a human genome with ultra-long reads
Jain, M., Koren, S., Miga, K. H., Quick, J., Rand, A. C., Sasani, T. A., Tyson, J. R., Beggs, A. D., Dilthey, A. T., Fiddes, I. T., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4060 · Cited by 1,892
Multi-platform discovery of haplotype-resolved structural variation in human genomes
Chaisson, M. J. P., Sanders, A. D., Zhao, X., Malhotra, A., Porubsky, D., Rausch, T., Gardner, E. J., Rodriguez, O. L., Guo, L., Collins, R. L., et al. (2019) · Nature Communications · doi:10.1038/s41467-018-08148-z · Cited by 891
De novo assembly of the cattle reference genome with single-molecule sequencing
Rosen, B. D., Bickhart, D. M., Schnabel, R. D., Koren, S., Elsik, C. G., Tseng, E., Rowan, T. N., Low, W. Y., Zimin, A., Couldrey, C., et al. (2020) · GigaScience · doi:10.1093/gigascience/giaa021 · Cited by 802
Piercing the dark matter: bioinformatics of long-range sequencing and mapping
Sedlazeck, F. J., Lee, H., Darby, C. A., & Schatz, M. C. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0003-4 · Cited by 530
The design and construction of reference pangenome graphs with minigraph
Li, H., Feng, X., & Chu, C. (2020) · Genome Biology · doi:10.1186/s13059-020-02168-z · Cited by 455
Self-citationEfficient assembly of nanopore reads via highly accurate and intact error correction
Chen, Y., Nie, F., Xie, S.-Q., Zheng, Y.-F., Dai, Q., Bray, T., Wang, Y.-X., Xing, J.-F., Huang, Z.-J., Wang, D.-P., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20236-7 · Cited by 446
Pangenomics enables genotyping of known structural variants in 5202 diverse genomes
Sirén, J., Monlong, J., Chang, X., Novak, A. M., Eizenga, J. M., Markello, C., Sibbesen, J. A., Hickey, G., Chang, P.-C., Carroll, A., et al. (2021) · Science · doi:10.1126/science.abg8871 · Cited by 400
BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files
Payne, A., Holmes, N., Rakyan, V., & Loose, M. (2019) · Bioinformatics · doi:10.1093/bioinformatics/bty841 · Cited by 326
GraphAligner: rapid and versatile sequence-to-graph alignment
Rautiainen, M., & Marschall, T. (2020) · Genome Biology · doi:10.1186/s13059-020-02157-2 · Cited by 242
The origin of domestication genes in goats
Zheng, Z., Wang, X., Li, M., Li, Y., Yang, Z., Wang, X., Pan, X., Gong, M., Zhang, Y., Guo, Y., et al. (2020) · Science Advances · doi:10.1126/sciadv.aaz5216 · Cited by 184
Long-range single-molecule mapping of chromatin accessibility in eukaryotes
Shipony, Z., Marinov, G. K., Swaffer, M. P., Sinnott-Armstrong, N. A., Skotheim, J. M., Kundaje, A., & Greenleaf, W. J. (2020) · Nature Methods · doi:10.1038/s41592-019-0730-2 · Cited by 160
Technology dictates algorithms: recent developments in read alignment
Alser, M., Rotman, J., Deshpande, D., Taraszka, K., Shi, H., Baykal, P. I., Yang, H. T., Xue, V., Knyazev, S., Singer, B. D., et al. (2021) · Genome Biology · doi:10.1186/s13059-021-02443-7 · Cited by 144
Chang, C.-H., & Larracuente, A. M. (2019) · Genetics · doi:10.1534/genetics.118.301765 · Cited by 141
An Artificial Chromosome for Data Storage
Chen, W., Han, M., Zhou, J., Ge, Q., Wang, P., Zhang, X., Zhu, S., Song, L., & Yuan, Y. (2021) · National Science Review · doi:10.1093/nsr/nwab028 · Cited by 136
New approaches for genome assembly and scaffolding
Rice, E. S., & Green, R. E. (2019) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-020518-115344 · Cited by 110
Wang, Y., Gallagher, L. A., Andrade, P. A., Liu, A., Humphreys, I. R., Turkarslan, S., Cutler, K. J., Arrieta-Ortiz, M. L., Li, Y., Radey, M. C., et al. (2023) · Cell · doi:10.1016/j.cell.2023.08.017 · Cited by 108
Genome-Wide Signatures of Adaptation to Extreme Environments in Red Algae
Cho, C. H., Park, S. I., Huang, T.-Y., Lee, Y., Ciniglia, C., Yadavalli, H. C., Yang, S. W., Bhattacharya, D., & Yoon, H. S. (2023) · Nature Communications · doi:10.1038/s41467-022-35566-x · Cited by 83
Genome assembly using quantum and quantum-inspired annealing
Boev, A. S., Rakitko, A. S., Usmanov, S. R., Kobzeva, A. N., Popov, I. V., Ilinsky, V. V., Kiktenko, E. O., & Fedorov, A. K. (2021) · Scientific Reports · doi:10.1038/s41598-021-88321-5 · Cited by 63
The complete telomere-to-telomere sequence of a mouse genome
Liu, J., Li, Q., Hu, Y., Yu, Y., Zheng, K., Li, D., Qin, L., & Yu, X. (2024) · Science · doi:10.1126/science.adq8191 · Cited by 57
Multiple genome alignment in the telomere-to-telomere assembly era
Kille, B., Balaji, A., Sedlazeck, F. J., Nute, M., & Treangen, T. J. (2022) · Genome Biology · doi:10.1186/s13059-022-02735-6 · Cited by 47
Siewert, L. K., Korotaev, A., Sedzicki, J., Fromm, K., Pinschewer, D. D., & Dehio, C. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2202059119 · Cited by 17
Le Luyer, J., Schull, Q., Auffret, P., Lopez, P., Crusot, M., Belliard, C., Basset, C., Carradec, Q., Poulain, J., Planes, S., et al. (2021) · Animal Microbiome · doi:10.1186/s42523-021-00097-1 · Cited by 16
Genomic insights into metabolic flux in hummingbirds
Gershman, A., Hauck, Q., Dick, M., Jamison, J. M., Tassia, M., Agirrezabala, X., Muhammad, S., Ali, R., Workman, R. E., Valle, M., et al. (2023) · Genome Research · doi:10.1101/gr.276779.122 · Cited by 5
Metadata
- Authors
- Li, H.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-03-19
- Volume
- 32
- Issue
- 14
- Pages
- 2103-2110
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2194172909
- Cited by
- 1,508
- References
- 5
- FWCI
- 42.89
- Type
- journal article
- Language
- en
- Open access
- bronze
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
