SMARTdenovo statistics

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Associated diseases

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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

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Versioning


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Maintainer


  • person_outline Jue Ruan <>

SMARTdenovo in publications

 (7)
PMCID: 5920178
PMID: 29700153
DOI: 10.1128/genomeA.00321-18

[…] 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 […]

PMCID: 5868456
PMID: 29616001
DOI: 10.3389/fmicb.2018.00478

[…] san diego, ca, united states). the paired-end short illumina reads were used to correct the long pacbio reads using proovread (), then the corrected pacbio reads were assembled de novo using smartdenovo., genomic dna from isolates gn26, gn28, and e20 was sequenced from a mate-pair libraries with an average insert size of 5 kb (ranging from 2 to 10 kb) using a miseq sequencer (illumina, […]

PMCID: 5824006
PMID: 29472323
DOI: 10.1128/genomeA.00018-18

[…] and nanopore technologies (, ). first, the long reads generated by the minion device (oxford nanopore technologies) were corrected using canu software (). the corrected reads were assembled using smartdenovo (https://github.com/ruanjue/smartdenovo), and the resulting assembly was then polished with the help of 2 × 150-bp paired-end reads generated by a miseq sequencer (illumina) with a genome […]

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

[…] 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 […]

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

[…] i.e. ∼25×) taking 15 mb as genome size estimate (supplemental material, table s1 in file s1), were subjected to four assemblers: abruijn (v0.3b) (), canu (v1.1) (), miniasm (v0.2-r137-dirty) (), and smartdenovo (https://github.com/ruanjue/smartdenovo). abruijn and miniasm were run with default parameters, while “genomesize=13 m, minreadlength=2500, mhapsensitivity=high, cormhapsensitivity=high, […]


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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) ?