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).

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. n/a
input_file input_file runtime parameter for tool HiFi Adapter Filter n/a
mode mode runtime parameter for tool Hifiasm n/a

Steps

ID Name Description
0 FASTQ input The FASTQ input to hifiasm can be sourced from the "BAM to FASTQ + QC" sub workflow.
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
cleanfastq cleanfastq n/a
blastout blastout n/a
blocklist blocklist n/a
stats stats n/a
raw_unitigs raw_unitigs n/a
processed_unitigs processed_unitigs n/a
primary_contig_graph primary_contig_graph n/a
alternate_contig_graph alternate_contig_graph n/a
outfile outfile n/a
outfile outfile n/a
outfile outfile n/a
outfile outfile n/a
outfile outfile n/a
outfile outfile n/a
outfile outfile n/a
out_fa out_fa n/a
outfile outfile n/a
stats stats n/a

Version History

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

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Frozen master c4797d8

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

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Views: 1357

Created: 26th Oct 2021 at 01:25

Last updated: 20th Sep 2022 at 02:01

Last used: 7th Oct 2022 at 15:39

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