Manual of AutoIMonitor-2.0

Introduction

IMonitor - analyze the sequence data of immune repertoire sequenced by NGS. If paired-end reads(FASTQ) as input, it will be merged to single sequence according to overlap region. FASTA sequence as input is acceptable. It provides re-alignment algorithm to identify accurately V,D,J alleles.Sequencing error will be corrected.CDR3 region can be identified by both VJ gene assignment and conserative region. deletion/insertion of VDJ will be identied and translate nucleotide into amino acid. Multiple statistics and graphs will be provied.
AutoIMonitor-2.0 - Based on IMonitor-MRD-1.1.0, AutoIMonitor-2.0 realizes the automated analysis process from the original sequencing data to the result report through one line of code. In the result report, we clearly showed the core results of the immune repertoire: In both Clone Identification^[1] and MRD^[2] report, we gave Top10 clone results included the its frequency and corresponding V/J gene information. At the same time, we gave the column diagram of Top10 clone in Clone Identification and the frequency change diagram of the Abnormal Clone^[3] in MRD.

System Requirement

It runs on 64-bit Linux systems. for 1Gb raw data as input, about maximum 2Gb memory would be required.

Perl、Python and R need to be installed for you system.

Installation

1. Before use it, perl(https://www.perl.org/get.html)
2. Before use it,Python(https://www.python.org/)
3. Before use it,R(http://www.r-project.org/) need to be installed. and provide the installation paths for parameter -Rs
4. Download the AutoIMonitor-2.0.tar.gz to your directory and uncompress it.

tar -zxvf AutoIMonitor-2.0.tar.gz

Environment Configuration

python_env

  In version 2.0, we need to install xlwt.

pip3 install xlwt

R_env

  In version 2.0, we need to install the packages as below.
  Note!!!The code has been added to each Rscript. You need to manually install the required package only if the software reports a "package does not exist" error.

cran_packages <- c('tidyverse',
                   'readxl',
                   'Cairo',
                   'cowplot',
                   'ggplot2',
                   'ggpubr',
                   'showtext',
                   'lubridate') 
for (pkg in cran_packages){
  if (! require(pkg,character.only=T) ) {
    install.packages(pkg,ask = F,update = F)
  }
}

Usage

You can get help documents to see more details.

###get help documents 
/Path/To/AutoIMonitor-2.0.sh 
/Path/To/AutoIMonitor-2.0.sh -h
/Path/To/AutoIMonitor-2.0.sh  --help

### AutoIMonitor-2.0---One line to complete the IMonitor analysis process
###
### Usage:
###   /Path/To/AutoIMonitor-2.0.sh <CloneType> <fq.gz1> <fq.gz2> <output path> <Prefix name> <Patient ID> <Date>
### 
### Options:
###   <CloneType>   IG orTR.Type of your sample.
###   <fq.gz1>  Path to R1.(sequence data)
###   <fq.gz2>  Path to R2.(sequence data)
###   <output path>  Path to output.（eg. /data/users/11-10)(Prefix name included)
###   <Prefix name>  The prefix of your outcome.(eg. 11-10)
###   <Patient ID>  As you like but the same patient must have the same ID.
###   <Date>  The sampling date.(eg.20211020)
###   
###   Learn more about AutoIMonitor-2.0 in Readme.

Example

/Path/To/AutoIMonitor-2.0.sh IG /Path/To/*R1.fq.gz /Path/To/*R2.fq.gz \
/Output/Path/11-10 11-10 Patient9527 20211021

Output

The primary directory is as follows. The red part is the new output generated by AutoIMonitor-2.0, and the black part is the original output of IMonitor. To learn more about output details generated by IMonitor, please to IMonitor(https://github.com/zhangwei2015/IMonitor) .

--Bin
--Align
--Result
--Figures
--
  --
  --
  --(MRD only)
  --(MRD only)
  --(Clone Identification only)

*Top10_CDR3_extract*：Top10 clone, its frequency and VJ information were recorded.(txt is convenient for programmers to use, and xls is convenient for viewing.)(May be csv is better.)
MRD.csv：If it's MRD, a csv file recording the change of abnormal clone frequency will be generated.
*FrequencyChange.png：If it's MRD, a png picture that visualizes the change of abnormal clone frequency will be generated.
*Merge_Clone_freq.png：If it's Clone Identification, a column diagram of Top10 clone will be generated.

--AutoIMonitor-2.0
  --

PatientInfo.csv：This file records the sample information for each run.

Cite

Zhang W, Du Y, Su Z, Wang C, Zeng X, Zhang R, Hong X, Nie C, Wu J, Cao H, et al: IMonitor: A Robust Pipeline for TCR and BCR Repertoire Analysis. Genetics 2015, 201:459-472.

···
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Footnote

1. Clone Identification：MRD_0 period, the patient underwent MRD detection for the first time, and the identified abnormal clone will be used as the index of subsequent MRD detection; ↩

2. MRD：Continuously monitor the frequency changes of abnormal clones identified in MRD_0; ↩

3. Abnormal Clone： ↩