PacBio HiFi genome assembly using hifiasm v2.1
v2.1.0

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Workflow Type: Galaxy
Stable

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

SEEK ID: https://dev.workflowhub.eu/workflows/1435?version=1

Inputs

ID Name Description Type
FASTQ input #main/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): blocklist #main/HiFi Adapter Filter on input dataset(s): blocklist n/a
  • File
HiFi Adapter Filter on input dataset(s): clean reads #main/HiFi Adapter Filter on input dataset(s): clean reads n/a
  • File
HiFi Adapter Filter on input dataset(s): contaminant blastout #main/HiFi Adapter Filter on input dataset(s): contaminant blastout n/a
  • File
HiFi Adapter Filter on input dataset(s): contaminant statistic #main/HiFi Adapter Filter on input dataset(s): contaminant statistic n/a
  • File
converted FASTA #main/converted FASTA n/a
  • File
metrics #main/metrics n/a
  • File
primary bandage image #main/primary bandage image n/a
  • File
primary bandage info #main/primary bandage info n/a
  • File

Version History

v2.1.0 (earliest) Created 2nd Jul 2025 at 08:13 by Johan Gustafsson

Add workflow v2.1


Frozen v2.1.0 499acb1
help Creators and Submitter
Creators
  • Gareth Price
  • Katherine Farquharson
Submitter
Citation
Price, G., & Farquharson, K. (2022). {PacBio-HiFi-genome-assembly-using-hifiasm} (Version 2.1.0). https://doi.org/["DOI goes here"]
License
GNU General Public License v3.0 or later
Activity

Views: 12   Downloads: 5   Runs: 0

Created: 2nd Jul 2025 at 08:13

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