Genome assembly evaluation pipeline

Postassm

This pipeline offers a variety of evaluations for genome assembly outcomes, such as accuracy, continuity, and completeness.

Quick start

change the config.yaml according to you environment.

  vim config.yaml

run with snakemake

   nohup snakemake -s postassm.smk -j 10 -k --ri >sublog 2>&1 &

run on a cluster

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

Configuration

project_name: project name

dir_work: work directory

software: software path (absolute path)

• busco:
• merqury:
• samtools:
• Rscript:
• xf_stat:
• seqtk:
• ...

lib_dir: database directory

• busco: path of BUSCO lib, for example /path/to/busco/datasets/mammalia_odb10
• busco_conf: config of BUSCO lib, for example /path/to/busco/conf/busco-master/config/config.ini

samples:

• sample1:
  • assm: sample1.fasta
  • meryl_lab: /path/to/meryl_db/sample1.meryl
• sample2:
  • assm: /path/to/sample2.fa
  • meryl_lab: /path/to/meryl_db/sample2.meryl
• ...

threads:

• busco: 48
• default: 2
• ...

Support tools

• BUSCO
• Merquery

Contribution

If you want to apply other tools to evaluate the genome, we encourage you to pull a request or email us.

Contact

• Peng Jia (pengjia@stu.xjtu.edu.cn)