MECAT: Fast Mapping, Error Correction, and De Novo Assembly for Single-molecule Sequencing Reads

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2017 Sep 26

PMID 28945707

Citations 186

Authors

Chuan-Le Xiao

Ying Chen

Shang-Qian Xie

Kai-Ning Chen

Yan Wang

Yue Han

Feng Luo

Zhi Xie

Affiliations

Soon will be listed here.

Abstract

We present a tool that combines fast mapping, error correction, and de novo assembly (MECAT; accessible at https://github.com/xiaochuanle/MECAT) for processing single-molecule sequencing (SMS) reads. MECAT's computing efficiency is superior to that of current tools, while the results MECAT produces are comparable or improved. MECAT enables reference mapping or de novo assembly of large genomes using SMS reads on a single computer.

Citing Articles

Evaluating long-read assemblers to assemble several aphididae genomes.

Burger N, Nicolis V, Botha A Brief Bioinform. 2025; 26(2).

PMID: 40079265 PMC: 11904405. DOI: 10.1093/bib/bbaf105.

A high-quality chromosome-level genome assembly of Pacific whiteleg shrimp (Penaeus vannamei).

Liao J, Lai Z, He C, Li G, Dong Z, Guo Y Sci Data. 2025; 12(1):340.

PMID: 40011501 PMC: 11865283. DOI: 10.1038/s41597-025-04673-x.

Benchmarking, detection, and genotyping of structural variants in a population of whole-genome assemblies using the SVGAP pipeline.

Hu M, Wan P, Chen C, Tang S, Chen J, Wang L bioRxiv. 2025; .

PMID: 39975360 PMC: 11839052. DOI: 10.1101/2025.02.07.637096.

xRead: a coverage-guided approach for scalable construction of read overlapping graph.

Kong T, Wang Y, Liu B Gigascience. 2025; 14.

PMID: 39960665 PMC: 11831799. DOI: 10.1093/gigascience/giaf007.

Towards the completion of Koch's postulates for the citrus huanglongbing bacterium, Liberibacter asiaticus.

Zheng D, Armstrong C, Yao W, Wu B, Luo W, Powell C Hortic Res. 2025; 11(3):uhae011.

PMID: 39896933 PMC: 11783299. DOI: 10.1093/hr/uhae011.

References

Langmead B, Salzberg S . Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9(4):357-9. PMC: 3322381. DOI: 10.1038/nmeth.1923. View

Berlin K, Koren S, Chin C, Drake J, Landolin J, Phillippy A . Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat Biotechnol. 2015; 33(6):623-30. DOI: 10.1038/nbt.3238. View

Chin C, Alexander D, Marks P, Klammer A, Drake J, Heiner C . Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods. 2013; 10(6):563-9. DOI: 10.1038/nmeth.2474. View

Koren S, Schatz M, Walenz B, Martin J, Howard J, Ganapathy G . Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol. 2012; 30(7):693-700. PMC: 3707490. DOI: 10.1038/nbt.2280. View

Chin C, Peluso P, Sedlazeck F, Nattestad M, Concepcion G, Clum A . Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods. 2016; 13(12):1050-1054. PMC: 5503144. DOI: 10.1038/nmeth.4035. View

Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G . Real-time DNA sequencing from single polymerase molecules. Science. 2008; 323(5910):133-8. DOI: 10.1126/science.1162986. View

Seo J, Rhie A, Kim J, Lee S, Sohn M, Kim C . De novo assembly and phasing of a Korean human genome. Nature. 2016; 538(7624):243-247. DOI: 10.1038/nature20098. View

Chaisson M, Tesler G . Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics. 2012; 13:238. PMC: 3572422. DOI: 10.1186/1471-2105-13-238. View

Gordon D, Huddleston J, Chaisson M, Hill C, Kronenberg Z, Munson K . Long-read sequence assembly of the gorilla genome. Science. 2016; 352(6281):aae0344. PMC: 4920363. DOI: 10.1126/science.aae0344. View

10.

Schadt E, Turner S, Kasarskis A . A window into third-generation sequencing. Hum Mol Genet. 2010; 19(R2):R227-40. DOI: 10.1093/hmg/ddq416. View

11.

Koch P, Platzer M, Downie B . RepARK--de novo creation of repeat libraries from whole-genome NGS reads. Nucleic Acids Res. 2014; 42(9):e80. PMC: 4027187. DOI: 10.1093/nar/gku210. View

12.

Koren S, Walenz B, Berlin K, Miller J, Bergman N, Phillippy A . Canu: scalable and accurate long-read assembly via adaptive -mer weighting and repeat separation. Genome Res. 2017; 27(5):722-736. PMC: 5411767. DOI: 10.1101/gr.215087.116. View

13.

Jain M, Fiddes I, Miga K, Olsen H, Paten B, Akeson M . Improved data analysis for the MinION nanopore sequencer. Nat Methods. 2015; 12(4):351-6. PMC: 4907500. DOI: 10.1038/nmeth.3290. View

14.

Shi L, Guo Y, Dong C, Huddleston J, Yang H, Han X . Long-read sequencing and de novo assembly of a Chinese genome. Nat Commun. 2016; 7:12065. PMC: 4931320. DOI: 10.1038/ncomms12065. View

15.

Loman N, Quick J, Simpson J . A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat Methods. 2015; 12(8):733-5. DOI: 10.1038/nmeth.3444. View

16.

Sovic I, Sikic M, Wilm A, Fenlon S, Chen S, Nagarajan N . Fast and sensitive mapping of nanopore sequencing reads with GraphMap. Nat Commun. 2016; 7:11307. PMC: 4835549. DOI: 10.1038/ncomms11307. View