SMARTdenovo statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SMARTdenovo
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Tool usage distribution map

This map represents all the scientific publications referring to SMARTdenovo per scientific context
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Associated diseases

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Popular tool citations

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SMARTdenovo specifications

Information


Unique identifier OMICS_19150
Name SMARTdenovo
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, Perl
Computer skills Advanced
Stability Stable
Maintained Yes

Subtools


  • wtclp
  • wtcns
  • wtgbo
  • wtmsa
  • wtzmo

Download


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Versioning


No version available

Maintainer


  • person_outline Jue Ruan

SMARTdenovo citations

 (6)
library_books

Genome Sequence of Australian Indigenous Wine Yeast Torulaspora delbrueckii COFT1 Using Nanopore Sequencing

2018
Genome Announc
PMCID: 5920178
PMID: 29700153
DOI: 10.1128/genomeA.00321-18

[…] 0× coverage) and an average length of 8,737 bp. Fast5 files were base called using Albacore version 2.0.2. Passed reads were trimmed for adapters using PoreChop version 0.2.3 and then assembled using SMARTdenovo version 1.0 (https://github.com/ruanjue/smartdenovo). Contigs obtained from the assembly were polished using Racon version 0.5.0 () and Nanopolish version 0.8.5 (). A final polish of the a […]

library_books

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

2017
F1000Res
PMCID: 5770995
PMID: 29375809
DOI: 10.5256/f1000research.12992.r24090

[…] obei and S. cerevisiae reads, it often produced an assembly with fewer indels and mismatches than others, often with higher contiguity – . These results are in line with the author’s own assessment . SMARTdenovo SMARTdenovo is a long read OLCassembly pipeline that was originally intended to work with PacBio reads, but has been shown to produce assemblies of reasonably high continuity from MinION r […]

library_books

The sea cucumber genome provides insights into morphological evolution and visceral regeneration

2017
PLoS Biol
PMCID: 5638244
PMID: 29023486
DOI: 10.1371/journal.pbio.2003790

[…] ge de novo assembly tool (SOAPdenovo) [], de Bruijn graph to Overlap-Layout-Consensus (DBG2OLC) (https://sourceforge.net/projects/dbg2olc/), FALCON (https://github.com/PacificBiosciences/FALCON), and SMARTdenovo (https://github.com/ruanjue/smartdenovo). The assembly result of SOAPdenovo was fragmented (1,165,887 contigs, N50 1,770 bp, and N90 230 bp). Compared with the SOAPdenovo assembly using on […]

library_books

High Quality de Novo Genome Assembly of the Dekkera bruxellensis Yeast Using Nanopore MinION Sequencing

2017
PMCID: 5633375
PMID: 28983066
DOI: 10.1534/g3.117.300128

[…] nged from 1.12 to 11% ( and Table S2 in File S1). Surprisingly, the assemblies constructed with miniasm were less complete, as >5% of the reads did not map back, compared to <1.5% for the ABruijn and SMARTdenovo assemblies.By comparing standard metrics and the proportion of unmapped reads, the most accurate assembly was obtained with the 20× 2D reads dataset combined with the SMARTdenovo assembler […]

library_books

De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms

2017
Sci Rep
PMCID: 5479803
PMID: 28638050
DOI: 10.1038/s41598-017-03996-z

[…] ased on an Overlap-Layout-Consensus (OLC) algorithm; ABruijn is based on a generalized De-Bruijn graph algorithm. All of them include a base-error correction step on the reads before assembling them. SMARTdenovo (available from https://github.com/ruanjue/smartdenovo) is also based on a OLC algorithm, but does not include a base-error correction step. Miniasm chooses the best path from a string gra […]

library_books

de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer

2017
GigaScience
PMCID: 5466710
PMID: 28369459
DOI: 10.1093/gigascience/giw018

[…] 8C, the only S. cerevisiae strain for which there is an established reference genome. We used different subsets of the reads as input to Canu (github commit ae9eecc), Miniasm (github commit 17d5bd1), SMARTdenovo (github commit 61cf13d), and ABruijn (github commit dc209ee), four assemblers that can take advantage of long reads. These subsets consisted of varying coverages of 1D, 2D, 2D pass reads, […]


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SMARTdenovo review

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Jiaxiang Hu

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Desktop
hello,
Does this software work well on ultra-long reads (nanopore) ?