Tool Overview

Tool overview

Software tools which genome sequencing use. It is a mirrored package of bioinformatics software. The tools can be programmed into the workflow in series or independently. We will provide a number of public tools, and users can create custom tools. All the tools are stored in a sequencing tool repository.

Tool format

name: <name>
version: <version>
image: <image>
cpu: <cpu>
memory: <memory>
description: <info>

Tool field

field required type description
name Yes string Name of tool, it must consist of lower case alphanumeric characters or ‘-’, start with an alphabetic character, and end with an alphanumeric character. The max length of name is 60 characters.
version Yes string Version of tool.
image Yes string Docker image name.
cpu No string cpu is the recommended cpu resources request for this tool to run. If we do not specify cpu request in the workflow, this value will be used. Format: “Number + Unit”.
  • The number can be decimals.
  • The unit is C or c.
For example, if the cpu required is 4C, you can fill in “4c” or “4C” here.
memory No string memory is the recommended memory resources request for this tool to run. If we do not specify memory request in the workflow, this value will be used. Format: “Number + Unit”.
  • The number can be decimals.
  • The unit is G or g.
For example, if the memory size required is 4G, you can fill in “4G” or “4g” here.
command No string The recommended command to use this tool.
description No string Information about this tool and instructions info for use. The max length of name is 255 characters.

Tool instance

A tool instance looks like this:

name: gatk
version: 4.0.9.0
image: gatk:4.0.9.0
cpu: 2c
memory: 2G
description: gatk

How to use tool

When you use genectl to submit genome sequencing workflow, you can specify what tool to use, the format is: “toolName:toolVersion”, and when the workflow is executing, it will use the real image to perform tht task. For example, when use sub job command,

genectl sub job /kubegene/bwa_help.sh --memory 1g --cpu 1 --tool bwa:0.7.12 --pvc pvc-gene

When use sub workflow command, the workflow will be:

...
  mergemappedbam:
    tool: 'bwa:0.7.12'
    resources:
      memory: 1G
    commands:
      - >-
        ls ${volume-path-tmp}/${sample}/${sample}.*.sort.bam >
        ${volume-path-tmp}/${sample}/mergelist.txt
    depends:
      - target: bwamapping
        type: whole
  samflagstat:
    tool: 'bwa:0.7.12'
    resources:
      memory: 1G
    commands:
      - >
        samtools merge -f -@ ${nthread} -b
        ${volume-path-tmp}/${sample}/mergelist.txt \

        ${volume-path-tmp}/${sample}/${sample}.sort.bam && \

        samtools flagstat ${volume-path-tmp}/${sample}/${sample}.sort.bam >
        ${volume-path-tmp}/${sample}/${sample}.sort.flagstat
    depends:
      - target: mergemappedbam
        type: whole
...

Common tools

There are some common tools that you can use to perform genome sequencing easily.

Tool name Tool description
gatk GATK: The Genome Analysis Tool Kit is a set of mutation detection software developed by the Broad Institute jointly developed by Harvard University and the Massachusetts Institute of Technology. It can perform error analysis and correction of base quality, detection of mutation areas, and filtering.
zsplit Zsplit, split the original fastq file into several subfiles.
bwa BWA, Burrows Wheeler Aligner and Samtools are classic genomic alignment applications that can be used to create reference alignments of reference genomes, then perform quick alignment of genomes based on indexes, and perform sam, bam format conversion, sequence ordering, etc. operating.