VGP hybrid scaffolding with HiC data Version 1
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Run on GalaxyPerforms scaffolding using HiC Data. Part of VGP assembly pipeline. The scaffolding can be performed on long read assembly contigs or on scaffolds (e.g.: Bionano scaffolds).
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Estimated genome size - Parameter File | n/a | Parameter file generated in the VGP Hifiasm workflow. Estimated reference genome size (in bp) for computing NGx statistics |
|
| HiC Forward reads | n/a | HiC forward reads in Fastq Format. The reads must be in the same order as reverse reads. |
|
| HiC reverse reads | n/a | HiC reverse reads in Fastq Format. The reads must be in the same order as forward reads. |
|
| Restriction enzyme sequences | n/a | File containing the list of restriction enzymes used by Arima technology, the sequences are separated by a comma. In the VGP project AWS, the restriction enzyme sequences can be found in the repository containing HiC data. |
|
| Scaffolded Assembly | n/a | Scaffold generated by "VGP Bionano" workflows or contigs Generated by the "VGP Hifiasm" workflow. |
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| Sequence graph - Optional | n/a | Sequence graphs encoded in GFA format. (-g) |
|
Steps
| ID | Name | Description |
|---|---|---|
| 10_Parse parameter value | n/a | n/a |
| 11_Parse parameter value | n/a | n/a |
| 12_Filter and merge | n/a | n/a |
| 13_bedtools BAM to BED | n/a | n/a |
| 14_PretextMap | n/a | n/a |
| 15_Sort | n/a | n/a |
| 16_Pretext Snapshot | n/a | n/a |
| 17_SALSA | n/a | n/a |
| 18_Busco | n/a | n/a |
| 19_BWA-MEM2 | n/a | n/a |
| 20_BWA-MEM2 | n/a | n/a |
| 21_Quast | n/a | n/a |
| 22_Filter and merge | n/a | n/a |
| 23_PretextMap | n/a | n/a |
| 24_Pretext Snapshot | n/a | n/a |
| 6_Input parameter | n/a | n/a |
| 7_Replace | n/a | n/a |
| 8_BWA-MEM2 | n/a | n/a |
| 9_BWA-MEM2 | n/a | n/a |
Version History
Version 1 (earliest) Created 6th Apr 2022 at 00:33 by Cristóbal Gallardo
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Creators and SubmitterViews: 6454 Downloads: 546 Runs: 4
Created: 6th Apr 2022 at 00:33
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Vertebrate Genomes ...
Related items
Teams: Vertebrate Genomes Pipelines in Galaxy
Organizations: Galaxy
https://orcid.org/0000-0001-6421-3484
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network, usegalaxy-eu, Intergalactic Workflow Commission (IWC)
Web page: https://galaxyproject.org/
This team and associated Galaxy workflows are maintained by the European Galaxy Team.
Space: Galaxy
Public web page: https://usegalaxy.eu
The Vertebrate Genomes Pipelines in Galaxy are intended to allow a user to generate high-quality near error-free assemblies of species from a user's own data or from the GenomeArk database.
