Workflow Type: Galaxy
Stable

PacBio HiFi genome assembly using hifiasm v2.1

General usage recommendations

Please see the Genome assembly with hifiasm on Galaxy Australia guide.

See change log

Acknowledgements

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
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 HiFi Adapter Filter toolshed.g2.bx.psu.edu/repos/galaxy-australia/hifiadapterfilt/hifiadapterfilt/2.0.0+galaxy0
2 hifiasm assembly toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.16.1+galaxy3
3 Haplotype resolved Bandage info toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1
4 Haplotype resolved 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 Processed unitig Bandage image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy3
7 Alternate assembly Bandage info toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1
8 Primary assembly Bandage info toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1
9 Convert primary assembly GFA to FASTA toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
10 Alternate assembly Bandage image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy3
11 Primary assembly Bandage image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy3
12 Primary assembly Fasta Statistics toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.3

Outputs

ID Name Description Type
HiFi Adapter Filter on input dataset(s): clean reads HiFi Adapter Filter on input dataset(s): clean reads n/a
  • File
HiFi Adapter Filter on input dataset(s): contaminant statistic HiFi Adapter Filter on input dataset(s): contaminant statistic n/a
  • File
HiFi Adapter Filter on input dataset(s): contaminant blastout HiFi Adapter Filter on input dataset(s): contaminant blastout n/a
  • File
HiFi Adapter Filter on input dataset(s): blocklist HiFi Adapter Filter on input dataset(s): blocklist n/a
  • File
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

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Frozen Version-1 9df3cb5
help Creators and Submitter
Citation
Price, G., & Farquharson, K. (2022). PacBio HiFi genome assembly using hifiasm v2.1. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.221.3
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Created: 26th Oct 2021 at 01:25

Last updated: 24th Oct 2022 at 02:55

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