Workflow Type: Galaxy
Frozen
Scaffolding using HiC data with YAHS
This workflow has been created from a Vertebrate Genomes Project (VGP) scaffolding workflow.
- For more information about the VGP project see https://galaxyproject.org/projects/vgp/.
- The scaffolding workflow is at https://dockstore.org/workflows/github.com/iwc-workflows/Scaffolding-HiC-VGP8/main:main?tab=info
- Please see that link for the workflow diagram.
Some minor changes have been made to better fit with TSI project data:
- optional inputs of SAK info and sequence graph have been removed
- the required input format for the genome is changed from gfa to fasta
- the estimated genome size now requires user input rather than being extracted from output of a previous workflow.
Inputs:
- assembly.fasta [note - scaffolding is done only one haplotype at a time. eg hap1 or primary]
- Concatenated HiC forward reads in fastqsanger.gz
- Concatenated HiC reverse reads in fastqsanger.gz
- Restriction enzyme sequence
- Estimated genome size (enter as integer)
- Lineage for busco
Outputs: the main outputs are:
- scaffolded_assmbly.fasta
- comparison of pre- post- scaffolding contact maps
Inputs
ID | Name | Description | Type |
---|---|---|---|
Estimated genome size in bp | Estimated genome size in bp | n/a |
|
HiC Forward reads | HiC Forward reads | Forward reads as a single dataset in fastq format |
|
HiC reverse reads | HiC reverse reads | Reverse reads as a single dataset in fastq format |
|
Lineage | Lineage | Taxonomic lineage for the organism being assembled for Busco analysis |
|
Restriction enzymes | Restriction enzymes | Restriction enzymes used in preparation of Hi-C libraries. |
|
assembly.fasta | assembly.fasta | n/a |
|
Steps
ID | Name | Description |
---|---|---|
6 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1 |
7 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1 |
8 | Filter and merge | toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1 |
9 | YAHS | toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy1 |
10 | PretextMap | toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1 |
11 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
12 | Pretext Snapshot | toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2 |
13 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
14 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
15 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
16 | Extract dataset | __EXTRACT_DATASET__ |
17 | gfastats_data_prep | n/a |
18 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0 |
19 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1 |
20 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1 |
21 | Cut | Cut1 |
22 | Cut | Cut1 |
23 | Filter and merge | toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1 |
24 | Nx Plot | toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1 |
25 | Size Plot | toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1 |
26 | bedtools BAM to BED | toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2 |
27 | PretextMap | toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1 |
28 | Sort | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1 |
29 | Pretext Snapshot | toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2 |
30 | Extract dataset | __EXTRACT_DATASET__ |
Outputs
ID | Name | Description | Type |
---|---|---|---|
YAHS on input dataset(s): Final scaffolds agp output | YAHS on input dataset(s): Final scaffolds agp output | n/a |
|
Reconciliated Scaffolds: gfa | Reconciliated Scaffolds: gfa | n/a |
|
Scaffold sizes for s2 | Scaffold sizes for s2 | n/a |
|
Reconciliated Scaffolds: fasta | Reconciliated Scaffolds: fasta | n/a |
|
Assembly Statistics for s2 | Assembly Statistics for s2 | n/a |
|
Pretext Map Before HiC scaffolding | Pretext Map Before HiC scaffolding | n/a |
|
Busco Summary | Busco Summary | n/a |
|
Busco Summary image | Busco Summary image | n/a |
|
Nx Plot | Nx Plot | n/a |
|
Size Plot | Size Plot | n/a |
|
Pretext Map After HiC scaffolding | Pretext Map After HiC scaffolding | n/a |
|
Version History
Version 1 (earliest) Created 21st Jun 2024 at 01:48 by Anna Syme
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VGP, Galaxy
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Citation
Project, V. G. P. (2024). TSI-Scaffolding-with-HiC (based on VGP-HiC-scaffolding). WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.1054.1
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Created: 21st Jun 2024 at 01:48
Last updated: 21st Jun 2024 at 01:56
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