Workflow Type: Galaxy
Stable

Assembly, visualisation and quality control workflow for high fidelity reads built from circular consensus sequence (PacBio HiFi) data.

Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)

Inputs

ID Name Description Type
FASTQ input FASTQ input The FASTQ input to hifiasm can be sourced from the "BAM to FASTQ + QC" sub workflow.
  • File

Steps

ID Name Description
1 hifiasm assembly toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.15.4+galaxy0
2 Haplotype resolved Bandage image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy3
3 Haplotype resolved Bandage info toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1
4 Processed unitig Bandage image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy3
5 Processed unitig Bandage info toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1
6 Alternate assembly Bandage info toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1
7 Primary assembly Bandage info toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1
8 Convert primary assembly GFA to FASTA toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
9 Primary assembly Bandage image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy3
10 Alternate assembly Bandage image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy3
11 Primary assembly Fasta Statistics toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.3

Outputs

ID Name Description Type
primary bandage info primary bandage info n/a
  • File
converted FASTA converted FASTA n/a
  • File
primary bandage image primary bandage image n/a
  • File
metrics metrics n/a
  • File

Version History

v2.1.0 (latest) Created 21st Oct 2022 at 06:13 by Johan Gustafsson

Add workflow v2.1


Frozen v2.1.0 499acb1

master @ c4797d8 Created 20th Sep 2022 at 01:59 by Johan Gustafsson

Add workflow v2


Frozen master c4797d8

Version 1 (earliest) Created 26th Oct 2021 at 01:25 by Johan Gustafsson

No revision comments

Frozen Version-1 9df3cb5
help Creators and Submitter
Activity

Views: 7786   Downloads: 594   Runs: 1

Created: 26th Oct 2021 at 01:25

Last updated: 24th Oct 2022 at 02:55

Annotated Properties
help Attributions

None

Total size: 153 KB
Powered by
(v.1.16.0-main)
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH