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Supernova

De novo genome assembler of 10X Genomics linked-reads

https://www.10xgenomics.com/

The module parses the reports from an assembly run. As a bare minimum it requires the file report.txt, found in the folder sampleID/outs/, to function. Note! If you are anything like the author (@remiolsen), you might only have files (often renamed to, e.g. sampleID-report.txt) lying around due to disk space limitations and for ease of sharing with your colleagues. This module will search for *report*.txt. If available the stats in the report file will be superseded by the higher precision numbers found in the file sampleID/outs/assembly/stats/summary.json. In the same folder, this module will search for the following plots and render them:

  • histogram_molecules.json -- Inferred molecule lengths
  • histogram_kmer_count.json -- Kmer multiplicity

This module has been tested using Supernova versions 1.1.4 and 1.2.0

Important note​

Due to the size of the histogram_kmer_count.json files, MultiQC is likely to skip these files. To be able to display these you will need to change the MultiQC configuration to allow for larger logfiles, see the MultiQC documentation. For instance, if you run MultiQC as part of an analysis pipeline, you can create a multiqc_config.yaml file in the working directory, containing the following line:

log_filesize_limit: 100000000

File search patterns​

supernova/kmers:
  contents: '"description": "kmer_count",'
  fn: histogram_kmer_count.json
  num_lines: 10
supernova/molecules:
  contents: '"description": "molecules",'
  fn: histogram_molecules.json
  num_lines: 10
supernova/report:
  contents: "- assembly checksum ="
  fn: "*report*.txt"
  num_lines: 100
supernova/summary:
  contents: '"lw_mean_mol_len":'
  fn: summary.json
  num_lines: 120