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PyMAP specifications

Information


Unique identifier OMICS_12943
Name PyMAP
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Amin Mahpour

Publication for PyMAP

PyMAP citations

 (2)
library_books

Sequence based ultra dense genetic and physical maps reveal structural variations of allopolyploid cotton genomes

2015
Genome Biol
PMCID: 4469577
PMID: 26003111
DOI: 10.1186/s13059-015-0678-1

[…] orporation of a framework of SSR markers from the existing linkage map [] and previously published chromosome naming systems []. To validate the linkage map, an independent program, CheckMatrix using PyMap BIT and REC scores, as described by Kozik [], was utilized. The recombination bin map was used to anchor scaffolds and calculate recombination rates. […]

library_books

High Resolution Genetic Mapping by Genome Sequencing Reveals Genome Duplication and Tetraploid Genetic Structure of the Diploid Miscanthus sinensis

2012
PLoS One
PMCID: 3306302
PMID: 22439001
DOI: 10.1371/journal.pone.0033821

[…] quencing errors and uncertainties caused by missing values and sequence duplication, the qualities of the final maps were carefully addressed and validated by an independent program CheckMatrix using PyMap BIT and REC scores as described by Kozik (http://www.atgc.org/XLinkage/). Any markers that were detected as having weak linkage positions were remapped by adjusting JoinMap parameters, or remove […]


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PyMAP institution(s)
Cancer Genetics Department, Roswell Park Cancer Institute, Buffalo, NY, USA

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