Gapless

Gapless is developed for genome assemblies merging with a hybrid assembly strategy

Authors

• Pengjia (pengjia@stu.xjtu.edu.cn)

License

Gapless is free for non-commercial use by academic, government, and non-profit/not-for-profit institutions. A commercial version of the software is available and licensed through Xi’an Jiaotong University. For more information, please contact with Peng Jia (pengjia@stu.xjtu.edu.cn) or Kai Ye (kaiye@xjtu.edu.cn).

Dependence

• System: Unix like system (test on ubuntu and centOS)
• Language: Python and snakemake
• Packages: snakemake, pysam, numpy and pandas
• Software: bwa, minimap2, samtools, minidot, jellyfish, ragtag, and seqtk

How to run Gapless?

1. Prepare you environment and install dependence

You can install the dependent packages and software with conda.

2. Download the pipeline and config the environment

Download the pipeline.

cd /path/to/gapless
git clone https://github.com/PengJia6/gapless.git

• Changed the software or packages path in conf/software.smk.
• Changed the parameters of the pipeline in conf/config.yaml.
• Changed the input path of you scaffolds and contigs in conf/scaffold.yaml.

3. Run the pipeline.

cd /path/to/gapless
snakemake  -s Snakefile -j 10 -k --ri -k 

If you want to run the pipeline in other directory, please copy the conf file in your directory and run with following command:

cd /m/work/directory
cp -r /path/to/gapless/gapless/conf .
snakemake -s /path/to/gapless/gapless/Snakefile -j 10 -k --ri 

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

If you have any questions, please contact with Peng Jia (pengjia@stu.xjtu.edu.cn) at Xi'an Jiaotong University.