Supernova is a de novo genome assembler for 10X Genomics linked-reads.
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:
The Supernova 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 If available the stats in the report file will be superseded by the higher precision numbers found in the file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
File search patterns
supernova/report: fn: "*report*.txt" num_lines: 100 contents: "- assembly checksum =" supernova/summary: fn: summary.json num_lines: 120 contents: '"lw_mean_mol_len":' supernova/molecules: fn: histogram_molecules.json num_lines: 10 contents: '"description": "molecules",' supernova/kmers: fn: histogram_kmer_count.json num_lines: 10 contents: '"description": "kmer_count",'