kmer counting - meryl
Version 1

Run on Galaxy

Workflow Type: Galaxy

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)

SEEK ID: https://workflowhub.eu/workflows/223?version=1

DOI: 10.48546/workflowhub.workflow.223.1

Inputs

ID	Name	Description	Type
Illumina reads R1	Illumina reads R1	n/a	File

ID	Name	Description
1	Meryl - count kmers	toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy4
2	Meryl - generate histogram	toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy4
3	Genomescope	toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy1

ID	Name	Description	Type
Meryl on input dataset(s): read-db.meryldb	Meryl on input dataset(s): read-db.meryldb	n/a	File
_anonymous_output_1	_anonymous_output_1	n/a	File
_anonymous_output_2	_anonymous_output_2	n/a	File
_anonymous_output_3	_anonymous_output_3	n/a	File
_anonymous_output_4	_anonymous_output_4	n/a	File
GenomeScope on input dataset(s) Transformed log plot	GenomeScope on input dataset(s) Transformed log plot	n/a	File
GenomeScope on input dataset(s) Log plot	GenomeScope on input dataset(s) Log plot	n/a	File
GenomeScope on input dataset(s) Linear plot	GenomeScope on input dataset(s) Linear plot	n/a	File
GenomeScope on input dataset(s) Transformed linear plot	GenomeScope on input dataset(s) Transformed linear plot	n/a	File