kmer counting - meryl
Version 1

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)


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


ID Name Description
0 Illumina reads R1
1 Meryl - count kmers
2 Meryl - generate histogram
3 Genomescope


ID Name Description Type
read_db read_db n/a
read_db_hist read_db_hist n/a
linear_plot linear_plot n/a
log_plot log_plot n/a
transformed_linear_plot transformed_linear_plot n/a
transformed_log_plot transformed_log_plot n/a
model model n/a
summary summary n/a
progress progress n/a

Version History

Version 1 (earliest) Created 8th Nov 2021 at 04:47 by Anna Syme

Added/updated 2 files

Open master abe51c7
help Creators and Submitter
Syme, A. (2021). kmer counting - meryl. WorkflowHub.

Views: 1151   Downloads: 3

Created: 8th Nov 2021 at 04:47

Last updated: 9th Nov 2021 at 01:10

Last used: 2nd Dec 2022 at 10:25

EDAM Properties
help Attributions


Total size: 369 KB
Powered by
Copyright © 2008 - 2022 The University of Manchester and HITS gGmbH

By continuing to use this site you agree to the use of cookies