使用IMonitor进行免疫组库分析

其实前面我们已经分享了MiXCR，还有igblast，这两个免疫组库上游分析软件已经够用，如下：

• 使用igblast进行免疫组库分析
• 使用MiXCR进行免疫组库分析

理论上不应该再介绍过多软件和流程，避免增加大家的认知负担，但是看到一个很新的文章发表在NC杂志，时间是11 April 2019，标题是 Multi-region sequencing unveils novel actionable targets and spatial heterogeneity in esophageal squamous cell carcinoma，该研究对33个食管癌病人进行了多位点取样，其中10个病人的64个样品进行了TCR的免疫组库测序，就使用了IMonitor作为分析工具。

• gDNA of 64 samples including the adjacent normal esophageal tissues, the regional tumors, the metastatic lymph nodes, and the PBMCs were extracted, and subjected to amplify TCR alpha and beta repertoire using multiple PCR.
• The V gene segments, J gene segments, and the whole complementarity determining region 3 (CDR3) were captured by PCR reactions.
• Amplification products were sequenced by xTen with 150-bp paired-end reads. Raw sequencing data were processed and filtered using IMonitor.
• Clean sequences were aligned to V and J germline alleles (IMGT database, www.imgt.org), and V and J gene segments were assigned for each clone.
• Meanwhile, the sequencing errors were corrected in terms of sequencing qualities and low-frequent sequences (≤2 in one million) were filtered out.

测序数据在：PRJNA511368 ，也是可以下载的，但是工具IMonitor其实引用并不多，是深圳华大基因员工开发。

IMonitor文章

首先下载和安装IMonitor

该软件的GitHub链接是：https://github.com/zhangwei2015/IMonitor

里面有一个压缩包，是打包好的软件，依赖于Linux系统的perl语言环境，

教程很简单：

FQ_run.sh:
        perl ../IMonitor.pl -a data/XHS_1.fq.gz -b data/XHS_2.fq.gz -A1 data/1.adapter.list.gz -A2 data/2.adapter.list.gz -o . -n XHS -T TRB -k 100 -r ../Ref/TRB -d -m -Rs /opt/blc/genome/biosoft/R/bin/Rscript
        FA_run.sh:
        perl ../IMonitor.pl -i data/XHS.merged.fa.gz  -o . -n XHS -T TRB -k 100 -r ../Ref/TRB -d -m -Rs /opt/blc/genome/biosoft/R/bin/Rscript

下载和安装该软件的代码是：

mkdir -p ~/biosoft/IMonitor
cd ~/biosoft/IMonitor 
perl -v
# This is perl 5, version 18, subversion 4 (v5.18.4)
git clone https://github.com/zhangwei2015/IMonitor

我们这里仍然是使用在前面我们认识的免疫组库测序数据，是人类的，MiSeq测序仪，PE300测序策略，TRB，DNA测序，进行示范。