本次分享一个Python基因组数据可视化工具figeno。

figeno擅长可视化三代long reads、跨区域基因组断点视图（multi-regions across genomic breakpoints）、表观组数据（HiC、ATAC-seq和ChIP-seq等）可视化、WGS中的CNV和SV可视化等。

figeno部分功能优秀于老牌工具如IGV，详细对比如下，

以下简单列举figeno使用案例：

支持三代测序数据可视化（Nanopore， PacBio数据），例如， base modification（5mC、hmC、6 mA、5mC、5hmC)）

支持多种格式数据类型输入

chr_axis： the genomic coordinates,

genes： annotated genes in the region

bed：additional custom genomic annotation

bigwig：visualization of epigenetic data types including ChIP-seq or ATAC-seq

hic：visualize HiC data (.cool format)等。

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支持多种格式publication-quality  fIgures导出

例如，bitmap (png)或者矢量图r(svg, pdf)等

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HiC data across breakpoints，展示跨基因组区域的染色质相互作用，

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WGS中的CNV和SV可视化

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asm

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Symmetrical layout for WGS

show the copy-number data on two rows, with the SVs in between

支持GUI界面

支持Python编程API

from figeno import figeno_make

config={"general":{"reference":"hg19","layout":"horizontal"}}
config["output"] = {"file":"figure.svg","dpi":200,"width":180}
config["regions"] = [{"chr":"17","start":7534342,"end":7628246}]
config["tracks"] = [
    {"type":"bigwig","file":"/path/to/H3K27ac.bigWig","color":"#e74c3c","label":"H3K27ac"},
    {"type":"bed","file":"/path/to/CGI.bed","color":"#34495e","label":"CpG islands"},
    {"type":"genes"},
    {"type":"chr_axis"}
  ]
figeno_make(config)

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参考：https://pubmed.ncbi.nlm.nih.gov/38857451/