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miniasm specifications


Unique identifier OMICS_11366
Name miniasm
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input format FASTA/FASTQ
Biological technology Pacific Biosciences, Oxford Nanopore
Operating system Unix/Linux
Programming languages C, Javascript, Shell (Bash)
License MIT License
Computer skills Advanced
Version 0.2
Stability Stable
Maintained Yes


No version available



  • person_outline Heng Li

Publication for miniasm

miniasm citations


A guide to sequence your favorite plant genomes

Appl Plant Sci
PMCID: 5895188
PMID: 29732260
DOI: 10.1002/aps3.1030

[…] l the reads constituting each contig to create a consensus sequence. PacBio or Nanopore long reads are best assembled by the OLC assemblers, such as Canu (Koren et al., ), FALCON (Chin et al., ), and miniasm (Li, ). Notably, by taking advantage of long reads, FALCON‐Unzip (Chin et al., ) can potentially phase and assemble individual haplotypes and would be particularly useful for highly heterozygo […]


Cultivation and Genomic Analysis of “Candidatus Nitrosocaldus islandicus,” an Obligately Thermophilic, Ammonia Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland

Front Microbiol
PMCID: 5817080
PMID: 29491853
DOI: 10.3389/fmicb.2018.00193

[…] ng the data from the Illumina and Nanopore sequencing with the hybrid assembler Unicycler (v. 0.4.1, ). The genome bins of the two contaminating organisms were assembled from the Nanopore reads using Miniasm () and polished twice with the Nanopore reads using Racon (). No other microbe, encoding genes indicative for ammonia-oxidation, was identified in either of the two metagenomes.The complete ge […]


High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

Nat Commun
PMCID: 5803254
PMID: 29416032
DOI: 10.1038/s41467-018-03016-2

[…] were extracted from base-called FAST5 files using poretools. Overlaps were generated using minimap with the recommended parameters (-Sw5 -L100 -m0). Genome assembly graphs (GFA) were generated using miniasm. Unitig sequences were extracted from GFA files. Canu assemblies were generated using the default parameters and the complete canu pipeline. Three rounds of consensus correction was performed […]


Nanopore DNA Sequencing and Genome Assembly on the International Space Station

Sci Rep
PMCID: 5740133
PMID: 29269933
DOI: 10.1038/s41598-017-18364-0

[…] We used Minimap v0.2-r124-dirty and Miniasm v0.2-r137-dirty as described in the github tutorial, using 8 threads ( Threeo assemblies were generated, (1) using 2D reads that mapped exclusively to Escherich […]


The long reads ahead: de novo genome assembly using the MinION

PMCID: 5770995
PMID: 29375809
DOI: 10.5256/f1000research.12992.r24090

[…] assembly error correction module, obtained an even more contiguous assembly with fewer predicted errors than either Canu or SMARTdenovo could, while still remaining faster than Canu alone . Minimap & Miniasm In terms of speed and computational efficiency, the OLC-based pipeline consisting of Minimap and Miniasm has a definite advantage over other existing tools – . This efficiency was reached thr […]


Alignment free sequence comparison: benefits, applications, and tools

Genome Biol
PMCID: 5627421
PMID: 28974235
DOI: 10.1186/s13059-017-1319-7

[…] shing. Integration of the MinHash Alignment Process with the Celera Assembler enabled reference-grade de novo assemblies of several eukaryotic genomes []. Another example includes currently developed Miniasm de novo assembler [], which uses an overlap-layout-consensus approach []. Miniasm requires all-versus-all read self-mappings as input, which can be obtained by the alignment-free Minimap tool. […]


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miniasm institution(s)
Medical Population Genetics, Broad Institute, Cambridge, MA, USA
miniasm funding source(s)
Supported by NHGRI U54HG003037 and NIH GM100233.

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