GPM specifications

Information


Unique identifier OMICS_12837
Name GPM
Alternative name Genome Puzzle Master
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Requirements
BLAST+, Scalable Vector Graphics, CGI, URI-Escape-XS, Math::Trig, JSON, jQuery, jQuery UI
Source code URL https://codeload.github.com/Jianwei-Zhang/LIMS/zip/master
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Jianwei Zhang

Publication for Genome Puzzle Master

GPM citations

 (2)
library_books

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

2017
Plant Biotechnol J
PMCID: 5425390
PMID: 27889940
DOI: 10.1111/pbi.12674

[…] Assembled PacBio contigs were assigned to chromosome pseudomolecules using Genome Puzzle Master [GPM; Zhang et al. ()]. Rice reference genome sequences were used to guide the process: Oryza sativa ssp. japonica var. Nipponbare genome was used for Taxon A and O. meridionalis was used for Taxon B. […]

library_books

Building two indica rice reference genomes with PacBio long read and Illumina paired end sequencing data

2016
Sci Data
PMCID: 5020871
PMID: 27622467
DOI: 10.1038/sdata.2016.76

[…] larization (minOverlap=500 bp, overlapIdentity=95%) and BAC Id assignments (minCloneTagNumber=5, tagMatchIdentity=100%, tagMatchPercent=80%; besMatchIdentity=98% if no WGP tag(s) is available).In the GPM ‘assemblyRun’ step for building BAC-based sequence contigs, the default parameters for merging two BAC sequences were ‘minOverlapSeqToSeq=1000 bp’ and ‘identitySeqToSeq=99%’, plus the overlaps wer […]

GPM institution(s)
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China; Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA; International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines
GPM funding source(s)
This study was supported by the Start-up Fund of the National Key Laboratory of Crop Genetic Improvement and the National Science Foundation Grant (#1026200).

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