Postassm

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

Quick start

1. change the config.yaml according to you environment.

     vim config.yaml 
   

2. run with snakemake

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

3. 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.

Citation

Jia P, Dong L, Yang X, Wang B, Wang T, Lin J, Wang S, Zhao X, Xu T, Che Y, et al: Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet. bioRxiv 2022:2022.2009.2008.504083. PDF

Contact

• Peng Jia (pengjia@stu.xjtu.edu.cn)