Workflow Type: Galaxy
Open
Stable
Optional workflow to purge duplicates from the contig assembly.
Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)
Inputs
ID | Name | Description | Type |
---|---|---|---|
HiFiASM 1o assembly | HiFiASM 1o assembly | Primary assembly input from hifiasm workflow, in FASTA format. | n/a |
HiFi reads as FASTQ | HiFi reads as FASTQ | Raw HiFi reads input, in FASTQ format. | n/a |
Steps
ID | Name | Description |
---|---|---|
0 | HiFiASM 1o assembly | Primary assembly input from hifiasm workflow, in FASTA format. |
1 | HiFi reads as FASTQ | Raw HiFi reads input, in FASTQ format. |
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 |
---|---|---|---|
split_fasta | split_fasta | n/a | |
alignment_output | alignment_output | n/a | |
alignment_output | alignment_output | n/a | |
stat_file | stat_file | n/a | |
pbcstat_cov | pbcstat_cov | n/a | |
pbcstat_wig | pbcstat_wig | n/a | |
hist | hist | n/a | |
calcuts_log | calcuts_log | n/a | |
calcuts_tab | calcuts_tab | n/a | |
purge_dups_log | purge_dups_log | n/a | |
purge_dups_bed | purge_dups_bed | n/a | |
get_seqs_hap | get_seqs_hap | n/a | |
get_seqs_purged | get_seqs_purged | n/a | |
stats | stats | n/a |
Version History
Version 1 (earliest) Created 15th Nov 2021 at 01:39 by Johan Gustafsson
Added/updated 2 files
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Views: 773 Downloads: 20
Created: 15th Nov 2021 at 01:39
Last updated: 15th Nov 2021 at 01:40
Last used: 26th Jun 2022 at 08:07


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