README.md

AssmPipe

Pipeline for genome assembly

Quick start

1. change the snakemake file according to you environment.

2. run with snakemake

   nohup snakemake -s pipeline.smk -j 10 -k --ri >sublog 2>&1 &
   nohup snakemake -s pipeline.smk -j 10 -k --ri --cluster "qsub -l nodes=1:ppn=20 -l walltime=999:00:00" >sublog 2>&1 & 

Support tools

• hifiasm
• hicanu
• flye
• shasta
• canu
• ...

Contribution

If you want to apply other tools to this pipeline, we encourage you to pull a request or email us.

Contact

• Peng Jia at Xi'an Jiaotong University (pengjia@stu.xjtu.edu.cn)