Workflow Type: Galaxy
General recommendations for using
Frozen
Frozen
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).
Inputs
ID | Name | Description | Type |
---|---|---|---|
HiFi reads as FASTQ | HiFi reads as FASTQ | n/a |
|
HiFiASM 1o assembly | HiFiASM 1o assembly | n/a |
|
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 |
|
_anonymous_output_2 | _anonymous_output_2 | n/a |
|
_anonymous_output_3 | _anonymous_output_3 | n/a |
|
_anonymous_output_4 | _anonymous_output_4 | n/a |
|
Purge overlaps on input dataset(s): purge_dups log file | Purge overlaps on input dataset(s): purge_dups log file | n/a |
|
Purge overlaps on input dataset(s): purge_dups bed file | Purge overlaps on input dataset(s): purge_dups bed file | n/a |
|
_anonymous_output_5 | _anonymous_output_5 | n/a |
|
_anonymous_output_6 | _anonymous_output_6 | n/a |
|
_anonymous_output_7 | _anonymous_output_7 | n/a |
|
Version History
v1.0.0 (latest) Created 17th Oct 2022 at 03:53 by Johan Gustafsson
Add workflow + update documentation
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v1.0.0
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Version 1 (earliest) Created 15th Nov 2021 at 01:39 by Johan Gustafsson
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Version-1
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Creators and Submitter
Creator
Additional credit
Gareth Price
Submitter
Tools
Citation
Price, G. (2022). Purge duplicates from hifiasm assembly v1.0. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.237.2
Activity
Views: 6282 Downloads: 417 Runs: 0
Created: 15th Nov 2021 at 01:39
Last updated: 17th Oct 2022 at 03:53
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