4 items tagged with 'VGP_curated'.
Purge Duplicate Contigs
Purge contigs marked as duplicates by purge_dups in a single haplotype(could be haplotypic duplication or overlap duplication) This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5)
Inputs
- Genomescope model parameters [txt] (Generated by the k-mer profiling workflow)
- Hifi long reads - trimmed [fastq] (Generated by Cutadapt in the contigging workflow)
- Assembly to purge (e.g. hap1) ...
Created: 15th Feb 2024 at 03:01, Last updated: 30th May 2024 at 11:36
Scaffolding with Bionano
Scaffolding using Bionano optical map data
Inputs
- Bionano data [cmap]
- Estimated genome size [txt]
- Phased assembly generated by Hifiasm [gfa1]
Outputs
- Scaffolds
- Non-scaffolded contigs
- QC: Assembly statistics
- QC: Nx plot
- QC: Size plot
Created: 4th Nov 2023 at 03:02, Last updated: 23rd Apr 2024 at 03:02
Purge contigs marked as duplicates by purge_dups (could be haplotypic duplication or overlap duplication). This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5)
Created: 31st Oct 2023 at 03:02, Last updated: 30th Apr 2024 at 03:02
Scaffolding using HiC data with YAHS.
Created: 27th Oct 2023 at 03:01, Last updated: 30th May 2024 at 11:35