github: https://github.com/CSB5/OPERA-MS

文章
文章：Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes
期刊：Nat Biotechnol
时间：2019

安装

conda安装：https://github.com/CSB5/OPERA-MS/issues/48

conda create -n operams python=3.9
conda activate operams
conda install perl-app-cpanminus
conda install -c compbiocore perl-switch perl==5.26.2
conda install -c bioconda perl-file-which perl-statistics-basic perl-statistics-r

mamba

mamba create -n operams python=3.9
conda activate operams
mamba install perl-app-cpanminus
mamba install -c compbiocore perl-switch perl==5.26.2
mamba install -c bioconda perl-file-which perl-statistics-basic perl-statistics-r

git clone https://github.com/CSB5/OPERA-MS.git
cd OPERA-MS
make
perl OPERA-MS.pl check-dependency

运行

source /hwfsxx1/ST_HN/P18Z10200N0423/chenjiahui/software/miniconda3_2/etc/profile.d/conda.sh
conda activate operams

route="/hwfsxx1/ST_HN/P18Z10200N0423/chenjiahui/software/OPERA-MS-OPERA-MS-0.9.0"

perl $route/OPERA-MS.pl \
--short-read1 00_rawdata/Y23030000014675.trimming.1.fq.gz \
--short-read2 00_rawdata/Y23030000014675.trimming.2.fq.gz \
--long-read 00_rawdata/Y23030000014675.rmhost.nanofilt.fq \
--no-ref-clustering \
--num-processors 24 \
--out-dir 01_assembly/05_operams