Minimap2: pairwise alignment for nucleotide sequences

Heng Li


Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms. Minimap2 is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database. It works with accurate short reads of ≥100 bp in length, ≥1 kb genomic reads at error rate ∼15%, full-length noisy Direct RNA or cDNA reads and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap cost for long insertions and deletions and introduces new heuristics to reduce spurious alignments. It is 3-4 times as fast as mainstream short-read mappers at comparable accuracy, and is ≥30 times faster than long-read genomic or cDNA mappers at higher accuracy, surpassing most aligners specialized in one type of alignment. Supplementary data are available at Bioinformatics online.


Jan 1, 1990·Bulletin of Mathematical Biology·O Gotoh
Jan 1, 1986·Bulletin of Mathematical Biology·S F Altschul, B W Erickson
Dec 15, 1982·Journal of Molecular Biology·O Gotoh
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Jul 17, 2004·Bioinformatics·Michael RobertsJames A Yorke
Feb 25, 2005·Bioinformatics·Thomas D Wu, Colin K Watanabe
Nov 4, 2005·Bioinformatics·Miao Zhang, Warren Gish
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jan 19, 2010·Bioinformatics·Heng Li, Richard Durbin
Jan 12, 2011·Nature Biotechnology·James T RobinsonJill P Mesirov
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Nov 7, 2012·Bioinformatics·Yukiteru OnoMichiaki Hamada
May 26, 2015·Nature Biotechnology·Konstantin BerlinAdam M Phillippy
Oct 9, 2015·Nature Biotechnology·Konstantin BerlinAdam M Phillippy
Nov 17, 2015·Bioinformatics·Bo LiuYadong Wang
Apr 16, 2016·Nature Communications·Ivan SovićNiranjan Nagarajan
Nov 1, 2016·Bioinformatics·Bo LiuYadong Wang
Apr 6, 2017·Bioinformatics·Hsin-Nan Lin, Wen-Lian Hsu
Apr 30, 2017·Bioinformatics·Martin Šošic, Mile Šikic
Jan 27, 2018·PLoS Computational Biology·Guillaume MarçaisAleksey Zimin
Feb 13, 2018·Nature Biotechnology·Miten JainMatthew Loose
Mar 6, 2018·BMC Bioinformatics·Hajime Suzuki, Masahiro Kasahara
May 2, 2018·Nature Methods·Fritz J SedlazeckMichael C Schatz

❮ Previous
Next ❯


Jan 23, 2019·Genome Biology and Evolution·Feng ZhangChao-Dong Zhu
Feb 5, 2019·Genome Biology and Evolution·Amit SinhaClotilde K S Carlow
Feb 3, 2019·Applied and Environmental Microbiology·Yun WuJustin Payne
Dec 12, 2018·International Journal of Cancer. Journal International Du Cancer·Kwai Fung HuiAlan Kwok Shing Chiang
Mar 7, 2019·G3 : Genes - Genomes - Genetics·Peter K NichollsDavid C Page
May 10, 2019·Scientific Reports·Anna L McNaughtonPhilippa C Matthews
Apr 18, 2019·Bioinformatics·Gregory Kucherov
May 28, 2019·Genome Research·Jun YoshimuraErich M Schwarz
May 23, 2019·Bioinformatics·Jia-Xing Yue, Gianni Liti
Nov 22, 2018·Bioinformatics·Alexander PayneMatthew Loose
May 10, 2019·Journal of Virology·Alistair B RussellJesse D Bloom
Jun 13, 2019·Genome Research·Wouter De CosterChristine Van Broeckhoven
May 6, 2019·Molecular Ecology Resources·Lukas Weilguny, Robert Kofler
Jun 21, 2019·Genome Biology and Evolution·Florencia Díaz-ViraquéCarlos Robello
Dec 28, 2018·Bioinformatics·Carlos de LannoyDick de Ridder
May 28, 2019·Molecular Plant-microbe Interactions : MPMI·Koichiro Ushijima, Mikihiro Yamamoto
Sep 5, 2019·Microbial Genomics·Nicola De Maio On Behalf Of The Rehab Consortium
Mar 6, 2018·BMC Bioinformatics·Hajime Suzuki, Masahiro Kasahara
Sep 4, 2019·Molecular Plant-microbe Interactions : MPMI·Chenming CuiDavid C Haak
Feb 13, 2018·Nature Biotechnology·Miten JainMatthew Loose
Sep 22, 2019·G3 : Genes - Genomes - Genetics·Jennafer A P HamlinDouda Bensasson
Sep 22, 2019·Applied and Environmental Microbiology·Sofiya G ShevchenkoEvgeni V Sokurenko
Aug 6, 2019·The Plant Journal : for Cell and Molecular Biology·Sarah N AndersonNathan M Springer
Sep 12, 2019·Nature Plants·Yongfeng ZhouBrandon S Gaut

❮ Previous
Next ❯

Related Concepts

Trending Feeds


Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.


Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.


Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.