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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

Versioning


No version available

Documentation


Maintainer


  • person_outline Shunichi Kosugi

Publication for GMcloser

GMcloser citations

 (8)
library_books

Whole genome sequencing of Leptospira interrogans from southern Brazil: genetic features of a highly virulent strain

2018
PMCID: 5722262
PMID: 29236923
DOI: 10.1590/0074-02760170130

[…] AST searches against the genome of L. interrogans strain Fiocruz L1-130 (GenBank: AE016823.1, AE016824.1) and ordered using CAR () based on this same reference genome. Assembly gaps were closed using GMCloser (), FGAP (), and manual curation with the CLC Genome Workbench (http://www.clcbio.com). Genome annotation was performed using Genix () and manually reviewed using Artemis (). In silico multil […]

library_books

Single molecule sequencing guided scaffolding and correction of draft assemblies

2017
BMC Genomics
PMCID: 5731603
PMID: 29244003
DOI: 10.1186/s12864-017-4271-8

[…] a 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 regions […]

library_books

The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies

2017
BMC Genomics
PMCID: 5603072
PMID: 28915793
DOI: 10.1186/s12864-017-4120-9

[…] Gaps in scaffolds were closed in two steps. GMcloser [] was executed in -long_read mode and default option with PacBio error-corrected reads larger than 500 bp. Then, GapCloser [] was used with the four Illumina LPR libraries with a pair number […]

library_books

Genome Analysis of Clostridium difficile PCR Ribotype 014 Lineage in Australian Pigs and Humans Reveals a Diverse Genetic Repertoire and Signatures of Long Range Interspecies Transmission

2017
Front Microbiol
PMCID: 5225093
PMID: 28123380
DOI: 10.3389/fmicb.2016.02138

[…] A5 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, ). Annotate […]

library_books

Approaches for in silico finishing of microbial genome sequences

2017
Genet Mol Biol
PMCID: 5596377
PMID: 28898352
DOI: 10.1590/1678-4685-GMB-2016-0230

[…] some steps of the program are executed serially, not in parallel, increasing the computation time. Sealer can be obtained from its GitHub repository https://github.com/bcgsc/abyss/tree/sealer-release.GMCLoser (): combines information from paired-end reads and an alternative assembly, or long-reads, to fill gaps inside scaffolds. Paired-end reads are mapped to the target, and alternative assembly w […]

library_books

Sequencing and comparative analyses of the genomes of zoysiagrasses

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

[…] iency using PE reads with 250–300 bases of read length. The scaffolds with the highest N50 values were obtained in Platanus for Z. japonica ‘Nagirizaki’ (Supplementary Table S2). After gap-closing by GMcloser, 334 Mb of scaffolds with an N50 length of 2.4 Mb were obtained (Table ). Ninety percent of the scaffolds (301 Mb) were included in the 167 longest scaffolds. According to the flow cytometry […]

Citations

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

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