Combined workflows for large genome assembly
Version 1

Workflow Type: Galaxy

Combined workflow for large genome assembly

The tutorial document for this workflow is here: https://doi.org/10.5281/zenodo.5655813

What it does: A workflow for genome assembly, containing subworkflows:

  • Data QC
  • Kmer counting
  • Trim and filter reads
  • Assembly with Flye
  • Assembly polishing
  • Assess genome quality

Inputs:

  • long reads and short reads in fastq format
  • reference genome for Quast

Outputs:

  • Data information - QC, kmers
  • Filtered, trimmed reads
  • Genome assembly, assembly graph, stats
  • Polished assembly, stats
  • Quality metrics - Busco, Quast

Options

  • Omit some steps - e.g. Data QC and kmer counting
  • Replace a module with one using a different tool - e.g. change assembly tool

Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)

Steps

ID Name Description
5 kmer counting - meryl c0b5fbb61b12154d
6 Data QC ae3b48869cad659b
7 Trim and filter reads - fastp 2ed2445df255451a
8 Assembly with Flye ec0fc1dbb6a13fe5
9 Assembly polishing 1fbcdce7d5823b15
10 Assess genome quality 9d0e6aba18484ea8

Version History

Version 1 (earliest) Created 8th Nov 2021 at 06:08 by Anna Syme

Added/updated 2 files


Open master 5ce10d2
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Citation
Syme, A. (2021). Combined workflows for large genome assembly. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.230.1
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Views: 1468   Downloads: 4

Created: 8th Nov 2021 at 06:08

Last updated: 11th Nov 2021 at 03:37

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