Workflow Type: Galaxy
Stable

Genome assessment post assembly

General usage recommendations

Please see the Genome assessment post assembly guide.

See change log

Attributions

The workflow & the doc_guidelines template used are supported by the Australian BioCommons via Bioplatforms Australia funding, the Australian Research Data Commons (https://doi.org/10.47486/PL105) and the Queensland Government RICF programme. Bioplatforms Australia and the Australian Research Data Commons are enabled by the National Collaborative Research Infrastructure Strategy (NCRIS).

Inputs

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

Steps

ID Name Description
1 Fasta Statistics toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0
2 Quast toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy1
3 Meryl toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy3
4 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy0
5 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3

Outputs

ID Name Description Type
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): Log Quast on input dataset(s): Log 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): HTML report Quast on input dataset(s): HTML report n/a
  • File
Meryl on input dataset(s): read-db.meryldb Meryl on input dataset(s): read-db.meryldb 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): size files Merqury on input dataset(s): size files n/a
  • File
Merqury on input dataset(s): stats Merqury on input dataset(s): stats 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
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

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
Citation
Price, G. (2022). Genome assessment post assembly. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.403.1
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Views: 5370   Downloads: 648   Runs: 6

Created: 7th Nov 2022 at 07:10

Last updated: 6th Aug 2024 at 11:04

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