安装
https://github.com/aljpetri/isONform?tab=readme-ov-file

#首先要安装pychopper
conda install -c nanoporetech -c conda-forge -c bioconda "nanoporetech::pychopper"
然后要安装isONform的三件套
pip install isONform
pip install isONclust
pip install isONcorrect

##
注意要保证上面全部软件都能直接运行

#然后克隆git项目
git clone https://github.com/aljpetri/isONform.git

就可以一键运行全流程，包括过滤/整合，获得isoform。
./isONform/isON_pipeline.sh --raw_reads pass.fq.gz  --outfolder isoform  --num_cores 60 --isONform_folder ~/disk1/fojiacao/RNA_ONT/isONform  --iso_abundance 2 --mode ont_with_pychopper

##注意输入的测序pass.fq.gz需要过滤过，这个一般测序公司都会帮过滤好，直接用就好

下面是各个参数的解释：

####ONT data
# ont_with_pychopper: the full pipeline is run in addition to pychopper (pychopper, isONclust,isONcorrect,isONform)
# ont_no_pychopper: only the isONpipeline is run without pychopper (isONclust,isONcorrect, isONform)

####PACBIO data
# pacbio: for PacBio data runs isONclust and isONform


###### test modes (only for internal use)
# analysis: analysis of ont data:  isONclust,isONcorrect and isONform are run (e.g. analyses on the paper)
# only_isonform: only isONform is run
#!/bin/bash

programname=$0
function usage {
    echo ""
    echo "Runs the full isON pipeline. Please make sure that the input file has been preprocessed with pychopper for ONT data "
    echo ""
    echo "usage: $programname --raw_reads string --outfolder string --num_cores integer --isONform_folder string  --iso_abundance integer --mode string"
    echo ""
    echo "  --raw_reads             absolute path to the input file (in fastq format)"
    echo "                          (example: /home/user/Rawdata/raw_reads.fq)"
    echo "  --outfolder             absolute path to the output folder (the folder in which all outputs are stored)"
    echo "                          (example: /home/user/analysis_output)"
    echo "  --num_cores             the number of processors the pipeline may use"
    echo "                          (example: 8)"
    echo "  --isONform_folder       the absolute path to the isONform installation on your machine (leave empty if you have installed isONform via pip)"
    echo "                          (example: /home/user/isONform )"
    echo "  --iso_abundance         threshold which denotes the minimum read support neccessary for an isoform to be called (also minimum number of reads per cluster in isONclust)"
    echo "                          (example: 5)"
    echo "  --mode                  Run mode of the pipeline, possible modes are 'ont_no_pyc' and 'ont_with_pc' for ont data and 'pacbio' for pacbio data"
    echo "                          (example: ont_no_pychopper/ont_with_pychopper/pacbio)"
    echo " For ONT data: use 'ont_no_pychopper' if you want to run the isON pipeline and pychopper, use 'ont_with_pychopper' if you only want to run the isON pipeline. Please run pychopper yourself before running the pipeline."
    echo ""
}