PacBio HiFi genome assembly using hifiasm v2.1
master @ c4797d8

v2.1.0 (latest)

master @ c4797d8

Version 1 (earliest)

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Run on Galaxy

Workflow Type: Galaxy

Stable

PacBio-HiFi-genome-assembly-using-hifiasm

General recommendations for using `PacBio-HiFi-genome-assembly-using-hifiasm`

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

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).

SEEK ID: https://workflowhub.eu/workflows/221?version=2

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/0.15.4+galaxy0
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	Alternate assembly Bandage image	toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy3
10	Convert primary assembly GFA to FASTA	toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
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): contaminant statistic	HiFi Adapter Filter on input dataset(s): contaminant statistic	n/a	File
HiFi Adapter Filter on input dataset(s): blocklist	HiFi Adapter Filter on input dataset(s): blocklist	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): clean reads	HiFi Adapter Filter on input dataset(s): clean reads	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