甲基化检测软件——Tombo

1.Tombo是一套工具，主要用于从纳米孔测序数据中鉴定修饰的核苷酸。Tombo还提供用于分析和可视化原始纳米孔信号的工具。

2.安装。

conda create -y -n ont-tombo  #创建ont-tombo虚拟环境并安装tombo

conda activate ont-tombo  #进入虚拟环境

conda install -c bioconda -n ont-tombo

conda deactivate  #退出虚拟环境

 3.关于tombo的使用参数。

tombo --help
usage: tombo [-h] [-v]
             {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot}
             ...

********** Tombo *********

Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data.

Tombo also provides tools for the analysis and visualization of raw nanopore signal.

Tombo command groups (additional help available within each command group):
	resquiggle               Re-annotate raw signal with genomic alignment from existing basecalls.
	preprocess               Pre-process nanopore reads for Tombo processing.
	filter                   Apply filter to Tombo index file for specified criterion.
	detect_modifications     Perform statistical testing to detect non-standard nucleotides.
	text_output              Output Tombo results in text files.
	build_model              Create canonical and alternative base Tombo models.
	plot                     Save plots to visualize raw nanopore signal or testing results.

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show Tombo version and exit.

 

4.人CpG甲基化检测。

# re-squiggle raw reads
tombo resquiggle path/to/fast5s/ reference.fasta \
   --processes 4 --num-most-common-errors 5

# run modified base detection
tombo detect_modifications alternative_model \
   --fast5-basedirs path/to/fast5s/ \
   --statistics-file-basename human_cpg_testing \
   --alternate-bases CpG --processes 4

# output to genome browser compatible format
tombo text_output browser_files \
   --fast5-basedirs path/to/fast5s/ \
   --statistics-filename human_cpg_testing.CpG.tombo.stats \
   --file-types coverage dampened_fraction \
   --browser-file-basename human_cpg_testing

产生的文件：

• human_cpg_testing.coverage.plus.bedgraph

• human_cpg_testing.coverage.minus.bedgraph

• human_cpg_testing.CpG.dampened_fraction_modified_reads.plus.wig

• human_cpg_testing.CpG.dampened_fraction_modified_reads.minus.wig

本文主要来自： https://github.com/nanoporetech/tombo