PacBio HiFi genome assembly using hifiasm (HiFi genome assembly stage 2)
Version 1

Workflow Type: Galaxy
Stable

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

Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)

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
dataset dataset runtime parameter for tool Fasta Statistics 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 hifiasm assembly toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.15.4+galaxy0
2 Haplotype resolved Bandage image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy3
3 Haplotype resolved Bandage info toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1
4 Processed unitig 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 Alternate assembly Bandage info toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1
7 Primary assembly Bandage info toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1
8 Convert primary assembly GFA to FASTA toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
9 Primary assembly Bandage image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy3
10 Alternate assembly Bandage image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy3
11 Primary assembly Fasta Statistics toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.3

Outputs

ID Name Description Type
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
out_fa out_fa n/a
outfile outfile n/a
outfile outfile n/a
stats stats n/a
Total size: 153 KB
help Creators and Submitter
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Activity

Views: 282   Downloads: 6

Created: 26th Oct 2021 at 01:25

Last updated: 9th Nov 2021 at 01:34

Last used: 26th Jan 2022 at 05:47

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Version History

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

Added/updated 2 files


Open master 9df3cb5

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