Purge duplicates from hifiasm assembly v1.0
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Run on usegalaxy.euOptional workflow to purge duplicates from the contig assembly.
Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| HiFi reads as FASTQ | HiFi reads as FASTQ | Raw HiFi reads input, in FASTQ format. |
|
| HiFiASM 1o assembly | HiFiASM 1o assembly | Primary assembly input from hifiasm workflow, in FASTA format. |
|
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
Frozen
v1.0.08ecf989
Version 1 (earliest) Created 15th Nov 2021 at 01:39 by Johan Gustafsson
Frozen
Version-1
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Creators and Submitter
Views: 4588
Created: 15th Nov 2021 at 01:39
Last updated: 17th Oct 2022 at 03:53
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HiFi genome assembl...
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The Australian BioCommons enhances digital life science research through world class collaborative distributed infrastructure. It aims to ensure that Australian life science research remains globally competitive, through sustained strategic leadership, research community engagement, digital service provision, training and support.
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