Genome-assessment-post-assembly

View on GitHub Download RO-Crate Run on Galaxy
Workflow Type: Galaxy
Stable

Post-genome assembly quality control workflow using Quast, BUSCO, Meryl, Merqury and Fasta Statistics

SEEK ID: https://workflowhub.eu/workflows/403?version=2

DOI: 10.48546/workflowhub.workflow.403.2

Inputs

ID Name Description Type
FASTA contigs - Primary Assembly FASTA contigs - Primary Assembly n/a
  • File
Raw reads Raw reads n/a
  • File

Steps

ID Name Description
2 Meryl toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6
3 Fasta Statistics toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0
4 Quast toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy1
5 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy0
6 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3

Outputs

ID Name Description Type
Meryl on input dataset(s): read-db.meryldb Meryl on input dataset(s): read-db.meryldb n/a
  • File
Fasta Statistics on input dataset(s): summary stats Fasta Statistics on input dataset(s): summary stats n/a
  • File
Quast on input dataset(s): PDF report Quast on input dataset(s): PDF report n/a
  • File
Quast on input dataset(s): HTML report Quast on input dataset(s): HTML report n/a
  • File
Quast on input dataset(s): tabular report Quast on input dataset(s): tabular report n/a
  • File
Quast on input dataset(s): Log Quast on input dataset(s): Log n/a
  • File
Busco on input dataset(s): full table Busco on input dataset(s): full table n/a
  • File
Merqury on input dataset(s): stats Merqury on input dataset(s): stats n/a
  • File
Merqury on input dataset(s): qv Merqury on input dataset(s): qv n/a
  • File
Merqury on input dataset(s): png Merqury on input dataset(s): png n/a
  • File
Merqury on input dataset(s): size files Merqury on input dataset(s): size files n/a
  • File
Merqury on input dataset(s): bed Merqury on input dataset(s): bed n/a
  • File
Merqury on input dataset(s): wig Merqury on input dataset(s): wig n/a
  • File

Version History

v2.0.5 (latest) Created 6th Aug 2024 at 11:04 by Anna Syme

Merge pull request #7 from AustralianBioCommons/supernord-workflow-name-fix

Update workflow name in ro-crate-metadata.json


Frozen v2.0.5 fe2213b

v2.0.4 Created 19th Apr 2024 at 02:56 by Anna Syme

Merge pull request #7 from AustralianBioCommons/supernord-workflow-name-fix

Update workflow name in ro-crate-metadata.json


Frozen v2.0.4 fe2213b

v2.0.2 Created 16th Apr 2024 at 08:19 by Johan Gustafsson

Update .lifemonitor.yaml


Frozen v2.0.2 4ad99a2

v1.1.0 Created 9th May 2023 at 01:59 by Johan Gustafsson

Add missing raw data input


Frozen v1.1.0 46d8253

v1.0.0 (earliest) Created 7th Nov 2022 at 07:10 by Johan Gustafsson

Update links


Frozen v1.0.0 efaf002
help Creators and Submitter
Creators
Submitter
Tools
QUAST
BUSCO
Merqury
FASTX-Toolkit
Citation
Price, G. (2023). Genome assessment post assembly v1.1. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.403.2
License
GNU General Public License v3.0 only
Activity

Views: 5080   Downloads: 590   Runs: 1

Created: 7th Nov 2022 at 07:10

Last updated: 6th Aug 2024 at 11:04

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