CGmapTools support BS-seq data analyses with command-lines

Citation

Weilong Guo * #, Ping Zhu *, et al. (2018), CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data, Bioinformatics, 34:381–387., (* joint first authors, # corresponding)
DOI:10.1093/bioinformatics/btx595

News

Advanced Features

1. Unified data formats: CGmap and ATCGmap

Use standard CGmap/ATCGmap formats as central format, for ease of sharing methylomes. ATCGmap/CGmap could be derived from BAM files, which are produced by BS-Seeker2 or Bismark

2. Command-lines: convenient for parallel processing and to be extended

Support both Linux and MAC; Support STDIN and STDOUT, so as to support pipe

3. Binary formats: support instantly retrieving

binary compressed formats: CGbz for CGmap, ATCGbz for ATCGmap

4. Novel SNV calling strategies with high precision

introduced ambigous genotype prediction, and significantly improve the precision especially in heterozygous SNVs

5. Support ASM analyses and visualizaiton

use precise heterozygous SNVs as input, designed Tanghulu plots for showing allele-specific DNA methylation on reads

6. DMR analysis use dynamic fragmentation strategy for

useful for low-coverage (WGBS) and fragmented (RRBS) DNA methylomes

7. Multiple-levels analysis and visualization

provide user-friendly functions for visualizing methylomes at multiple levels, such as design a Tanghulu plot for visualizing methylation status on original reads, and design a Lollipop plot to reveal both lowly-covered cytosines and un-methylated cytosines in a local region

Example

$ cgmaptools -h
Program : cgmaptools (Tools for analysis in CGmap/ATCGmap format)
Version:  0.0.6
Usage:    cgmaptools <command> [options]
Commands:
  -- File manipulation
     convert     + data format conversion tools
     fetch       + fetch a region by random accessing
     refill        refill the missing columns
     intersect     intersect two files
     merge2      + merge two files into one
     mergelist   + merge a list of files
     sort          sort lines by chromosome and position
     split       + split file by chromosomes
     select      + select lines by region/site
  -- SNV analysis
     snv           snv analysis
  -- Methylation analysis
     dms           differentially methylated site analysis
     dmr           differentially methylated region analysis
     asm           allele-specific methylation analysis
     mbed          average methylation level in regions
     mbin        * single sample, mC levels in bins
     mmbin         multiple samples, mC levels in bins
     mfg           methlation levels across fragmented region
     mstat       * methyaltion statistic
     mtr           methylation level to each region
  -- Coverage analysis
     oac        +* overall coverage (for ATCGmap)
     mec        +* methylation effective coverage (for CGmap)
  -- Graph related functions
     lollipop    * show local mC levels as lollipop bars
     heatmap     * global mC distribution for multiple samples
     fragreg     * show mC profile across fragmented regions
     tanghulu    * show local mapped reads in Tanghulu shape
  -- Other Utils
     findCCGG      get MspI cutting sites for RRBS
     bed2fragreg   get fragmented region based on region
Note:
  Commands support figures generation are marked with "*"
  Commands contain sub-commands are marked with "+"
Authors:
  GUO, Weilong; guoweilong@126.com;  http://guoweilong.github.io
  ZHU, Ping; pingzhu.work@gmail.com; http://perry-zhu.github.io

#Authors

#Who is watching CGmapTools?