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CGmapTools

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Provides a standard for bisulfite sequencing data related manipulation. CGmapTools is a command-line bisulfite sequencing analysis toolkit with enhanced features on single-nucleotide variant (SNV) calling and allele specific methylations and visualizations. It includes modules for better data storage, extraction, visualization and improved performance in single-nucleotide polymorphism (SNP) calling.

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2 user reviews

2 user reviews

BS-Seeker2's avatar image

BS-Seeker2

CGmapTools provides seamless tools for downstream analysis of BS-Seeker2.
It can also accept BAM files generated by BS-Seeker2 and Bismark.

Weilong Guo's avatar image Weilong Guo's country flag

Weilong Guo

CGmapTools is a command-line package, can be available for SNV calling analysis, Allele-specific methylation analysis, coverage analysis, differentially methylation analysis, and bin-wise, region-wise, chromosome-wise, and context-wise DNA methylation analysis.
It also designed binary CGbz format to improve storage and accessing large DNA methylome data.
CGmapTools also support lots of figure generations.

CGmapTools forum

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CGmapTools classification

  • Animals
  • Archaebacteria
  • Eubacteria
  • Fungi
  • Plants
  • Viruses

CGmapTools specifications

Software type:
Toolkit/Suite
Restrictions to use:
Academic or non-commercial use
Input format:
BAM, CGmap, ATCGmap
Output format:
PNG, PDF, XLS
Operating system:
Unix/Linux, Mac OS
License:
MIT License
Version:
0.0.3
High performance computing:
No
Registration required:
No
Availability:
Yes
Interface:
Command line interface
Input data:
Alignment result, DNA methylome
Output data:
figures, mate-analysis result
Biological technology:
Illumina
Programming languages:
C, C++, Perl, Python, R
Computer skills:
Advanced
Stability:
Beta
Free trial:
Yes
Maintained:
Yes

CGmapTools distribution

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CGmapTools support

Maintainer

Additional information

https://cgmaptools.github.io/cgmaptools_documentation/what-is-cgmaptools.html

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