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Xengsort

Fast xenograft read sorter based on space-efficient k-mer hashing

https://gitlab.com/genomeinformatics/xengsort

The module parses results generated by the xengsort classify command.

Note: MultiQC parses the standard output from xengsort, hence one has to redirect command line output to a file in order to use it with the MultiQC module. Also note that the tool does not register any sample name information in the output, so MultiQC attempts to fetch the sample name from the file name by default. Example command that would help MultiQC recognize data for a sample named "SAMPLE":

xengsort classify --index myindex       --fastq paired.1.fq.gz --pairs paired.2.fq.gz       --prefix myresults       --classification count       > SAMPLE.txt

File search patterns​

xengsort:
  contents: "# Xengsort classify"
  num_lines: 2