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GMcloser specifications

Information


Unique identifier OMICS_00042
Name GMcloser
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Pacific Biosciences, Oxford Nanopore
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Shunichi Kosugi <>

Publication for GMcloser

GMcloser in pipeline

2016
PMCID: 4833424
PMID: 26975196
DOI: 10.1093/dnares/dsw006

[…] n50 values than the other assemblers. this may be because only a single mp library was generated for these species. the final assemblies for ‘wakaba’ and ‘zanpa’ were generated by gap-closing with gmcloser and resulted in 563 mb (n50 length, 109 kb) and 397 mb (n50 length, 111 kb), respectively (table ). as with ‘nagirizaki’, the genome size of ‘zanpa’ estimated by flow cytometry (370 mb; 0.76 […]


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GMcloser in publications

 (6)
PMCID: 5731603
PMID: 29244003
DOI: 10.1186/s12864-017-4271-8

[…] comparison. individual components of this method are also related to prior work in assembly improvement. for example, our scaffolding step is similar to the likelihood-based gap closing approach of gmcloser [], similar to [], as well as the recently reported scaffmatch []. in contrast, we compute overlaps between sms reads in order to more accurately weight the connections between genome […]

PMCID: 5225093
PMID: 28123380
DOI: 10.3389/fmicb.2016.02138

[…] pipeline (coil et al., ). abacas v1.3.1 (assefa et al., ) was used to order and orientate contigs relative to the genome of reference strain cd630 (genbank accession am180355.1, st54, clade 1) and gmcloser v1.3 (kosugi et al., ) was used for gap closure and contig extension. finally, ab initio annotation was performed using the rapid genome annotation pipeline prokka v1.11 (seemann, ). […]

PMCID: 5596377
PMID: 28898352
DOI: 10.1590/1678-4685-GMB-2016-0230

[…] approach, which is employed by fgap () and gapblaster (), uses an auxiliary set of contigs to find sequences that may fill the region based on local alignment. finally, hybrid approaches, such as gmcloser (), may use a combination of paired-end data, alternative assemblies and long reads in the gap-closing process., gapcloser (): is part of the soapdenovo software package (). this module uses […]

PMCID: 4833424
PMID: 26975196
DOI: 10.1093/dnares/dsw006

[…] using opera, v2.0. gaps in the ‘wakaba’ and ‘zanpa’ scaffolds were filled by a sequential treatment with the two contig sets (the discovar de novo-contig set and the fermi-contig set) using gmcloser., for rna-seq analysis, pe libraries were prepared using 1 µg of total rna extracted from young leaves and roots of ‘nagirizaki’ using the truseq stranded total rna with ribo-zero plant kit […]

PMCID: 4786656
PMID: 26966200
DOI: 10.1128/genomeA.00089-16

[…] (). further automated scaffolding with opera v2.0 () and manual refinement of the assembly () using the mate-pair data were additionally performed. gaps in the resulting scaffolds were closed using gmcloser v1.5 () and gapfiller v1.11 (). genome annotation was performed within the integrated microbial genomes (img) platform ()., the final high-quality, nearly complete draft assembly consists […]


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GMcloser institution(s)
Kazusa DNA Research Institute, Kisarazu, Chiba, Japan

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