Purge duplicates from hifiasm assembly v1.0
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Run on GalaxyOptional 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
d37b742
Creators and Submitter
Views: 6819 Downloads: 492 Runs: 0
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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