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)

Inputs

ID Name Description Type
long reads long reads n/a n/a
R1 R1 n/a n/a
R2 R2 n/a n/a
minimap settings (for long reads) minimap settings (for long reads) n/a n/a
Reference genome for Quast Reference genome for Quast n/a n/a
Data QC Data QC n/a n/a
Assembly with Flye Assembly with Flye n/a n/a

Steps

ID Name Description
0 long reads
1 R1
2 R2
3 minimap settings (for long reads)
4 Reference genome for Quast
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
Total size: 617 KB
help Creators and Submitter
Creator
Submitter
Citation
Syme, A. (2021). Combined workflows for large genome assembly. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.230.1
Activity

Views: 255   Downloads: 1

Created: 8th Nov 2021 at 06:08

Last updated: 11th Nov 2021 at 03:37

Last used: 26th Jan 2022 at 19:37

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

Added/updated 2 files


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