Research Object Crate for Purge duplicates from hifiasm assembly v1.0 (HiFi genome assembly stage 3)
Version 1

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Workflow Type: Galaxy

Optional workflow to purge duplicates from the contig assembly.

Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)

SEEK ID: https://dev.workflowhub.eu/workflows/233?version=1

Inputs

ID	Name	Description	Type
HiFi reads as FASTQ	HiFi reads as FASTQ	Raw HiFi reads input, in FASTQ format.	File
HiFiASM 1o assembly	HiFiASM 1o assembly	Primary assembly input from hifiasm workflow, in FASTA format.	File

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

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

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Frozen Version-1 ab0934a

Creators and Submitter

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Gareth Price

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Created: 23rd Nov 2021 at 10:26

Last updated: 26th Jan 2022 at 12:07