Research Object Crate for kmer counting - meryl

Kmer counting step, can run alone or as part of a combined workflow for large genome assembly. * What it does: Estimates genome size and heterozygosity based on counts of kmers * Inputs: One set of short reads: e.g. R1.fq.gz * Outputs: GenomeScope graphs * Tools used: Meryl, GenomeScope * Input parameters: None required * Workflow steps: The tool meryl counts kmers in the input reads (k=21), then converts this into a histogram. GenomeScope: runs a model on the histogram; reports estimates. k-mer size set to 21. * Options: Use a different kmer counting tool. e.g. khmer. Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)

Author

Anna Syme

License

Apache-2.0

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