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

Workflow Type: Galaxy
Stable

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

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 (earliest) Created 21st Mar 2023 at 02:48 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}. https://doi.org/["DOI goes here"]
Activity

Views: 553   Downloads: 127

Created: 21st Mar 2023 at 02:48

Annotated Properties
Operation annotations
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