This component performs mapping (using bowtie2 and samtools) against a plasmid database in order to find plasmids contained in high throughoput sequencing data. Then, the resulting file can be imported into pATLAS.


  • pATLAs documentation can be found here.
  • bowtie2 documentation can be found here.
  • samtools documentation can be found here.

Input/Output type

  • Input type: fastq
  • Output type: json


  • max_k: Sets the k parameter for bowtie2 allowing to make multiple mappings of the same read against several hits on the query sequence or sequences. Default: 10949.
  • trim5: Sets trim5 option for bowtie. This will become legacy with QC integration, but it enables to trim 5’ end of reads to be mapped with bowtie2. Default: 0
  • lengthJson: A dictionary of all the lengths of reference sequences. Default: ‘jsons/*_length.json’ (from docker image).
  • refIndex: Specifies the reference indexes to be provided to bowtie2. Default: ‘/ngstools/data/indexes/bowtie2idx/bowtie2.idx’ (from docker image).
  • samtoolsIndex: Specifies the reference indexes to be provided to samtools. Default: ‘/ngstools/data/indexes/fasta/samtools.fasta.fai’ (from docker image).

Published results

  • results/mapping/: A JSON file that can be imported to pATLAS with the results from mapping.

Published reports


Default directives

  • mappingBowtie:
    • container: flowcraft/mapping-patlas
    • version: 1.6.0-1
  • samtoolsView:
    • container: flowcraft/mapping-patlas
    • version: 1.6.0-1
  • jsonDumpingMapping:
    • container: flowcraft/mapping-patlas
    • version: 1.6.0-1