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)

Inputs

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

Steps

ID Name Description
0 Illumina reads R1
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

Outputs

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


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Syme, A. (2021). kmer counting - meryl. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.223.1
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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

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