Purge duplicates from hifiasm assembly v1.0
v1.0.0 (latest)

v1.0.0 (latest)

Version 1 (earliest)

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Run on Galaxy

Workflow Type: Galaxy

Stable

Purge-duplicates-from-hifiasm-assembly

General recommendations for using `Purge-duplicates-from-hifiasm-assembly`

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/237?version=2

DOI: 10.48546/workflowhub.workflow.237.2

Inputs

ID	Name	Description	Type
HiFi reads as FASTQ	HiFi reads as FASTQ	n/a	File
HiFiASM 1o assembly	HiFiASM 1o assembly	n/a	File

Steps

ID	Name	Description
2	Step 1. Base-level coverage	toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy3
3	Step 1. Run minimap2 to align pacbio data and generate paf files,	toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.20+galaxy2
4	Step 1. Split an assembly and do a self-self alignment	toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.20+galaxy2
5	Step 1. then calculate read depth histogram and base-level read depth.	toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy3
6	Step 2. Purge haplotigs and overlaps	toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy3
7	Step 3. Get purged primary and haplotig sequences from draft assembly	toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy3
8	Haplotype fasta	toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.3

Outputs

ID	Name	Description	Type
_anonymous_output_1	_anonymous_output_1	n/a	File
_anonymous_output_2	_anonymous_output_2	n/a	File
_anonymous_output_3	_anonymous_output_3	n/a	File
_anonymous_output_4	_anonymous_output_4	n/a	File
Purge overlaps on input dataset(s): purge_dups log file	Purge overlaps on input dataset(s): purge_dups log file	n/a	File
Purge overlaps on input dataset(s): purge_dups bed file	Purge overlaps on input dataset(s): purge_dups bed file	n/a	File
_anonymous_output_5	_anonymous_output_5	n/a	File
_anonymous_output_6	_anonymous_output_6	n/a	File
_anonymous_output_7	_anonymous_output_7	n/a	File