hi-c-contact-map-for-assembly-manual-curation/main

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Workflow Type: Galaxy

This workflow generates Hi-C contact maps for genome assemblies in the Pretext format. It is compatible with one or 2 haplotypes. It includes tracks for PacBio read coverage, Gaps, and telomeres. The Pretext files can be open in PretextView for the manual curation of genome assemblies.

SEEK ID: https://workflowhub.eu/workflows/1327?version=4

Inputs

ID Name Description Type
Do you want to add suffixes to the scaffold names? Do you want to add suffixes to the scaffold names? Add haplotype suffix to the scaffold names (e.g. Scaffold_1_hap1). Necessary if the assemblies don't already have a marker of haplotype in the scaffold names.
  • boolean
Do you want to trim the Hi-C data? Do you want to trim the Hi-C data? Trim 5 bases at the beginning of each read. Use with Arima Hi-C data if the Hi-C map looks "noisy".
  • boolean
First Haplotype suffix First Haplotype suffix Suffix added to scaffolds belonging to haplotype 1.
  • string?
Haplotype 1 Haplotype 1 Assembly for Haplotype 1.
  • File
Haplotype 2 Haplotype 2 Assembly for Haplotype 2. If "Will you use a second haplotype?" is set to "no", use haplotype 1 here.
  • File
Hi-C reads Hi-C reads Paired Collection containing the Hi-C reads.
  • File[]
PacBio reads PacBio reads n/a
  • File[]
Second Haplotype suffix Second Haplotype suffix Suffix added to contigs belonging to haplotype 2.
  • string?
Telomere repeat to suit species Telomere repeat to suit species The default value is set for vertebrate genomes (CCCTAA).
  • string?
Will you use a second haplotype? Will you use a second haplotype? n/a
  • boolean

Steps

ID Name Description
10 Hap2 not provided toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
11 Add suffix to 2 haplotypes n/a
12 concatenate HiFi toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy0
13 Add Suffix 1 haplotype n/a
14 Pick Assembly toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
15 Trim and Align Hi-C paired collection n/a
16 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
17 seqtk_telo toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_telo/1.4+galaxy0
18 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1
19 PretextMap toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1
20 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1
21 Cut Cut1
22 bamCoverage toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.4+galaxy0
23 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1
24 Add Coverage Track toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0
25 Test if telomere track is empty param_value_from_file
26 False if telomere track is empty toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
27 Add telomere track toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0
28 Pick parameter value toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
29 Add gaps track toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0
30 Pretext Snapshot toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0
31 Extract dataset __EXTRACT_DATASET__

Outputs

ID Name Description Type
Assembly for curation Assembly for curation n/a
  • File
Merged Hi-C Alignments Merged Hi-C Alignments n/a
  • File
Gaps Bed Gaps Bed n/a
  • File
Seqtk-telo Output Seqtk-telo Output n/a
  • File
Gaps Bedgraph Gaps Bedgraph n/a
  • File
BigWig Coverage BigWig Coverage n/a
  • File
Telomeres Bedgraph Telomeres Bedgraph n/a
  • File
Pretext All tracks Pretext All tracks n/a
  • File
Pretext Snapshot With tracks Pretext Snapshot With tracks n/a
  • File

Version History

v1.0beta4 (latest) Created 9th Apr 2025 at 03:01 by WorkflowHub Bot

Updated to v1.0beta4


Frozen v1.0beta4 942f789

v1.0beta3 Created 8th Apr 2025 at 03:01 by WorkflowHub Bot

Updated to v1.0beta3


Frozen v1.0beta3 22438d9

v1.0beta2 Created 29th Mar 2025 at 03:01 by WorkflowHub Bot

Updated to v1.0beta2


Frozen v1.0beta2 7444f24

v1.0beta1 (earliest) Created 29th Mar 2025 at 03:01 by WorkflowHub Bot

Updated to v1.0beta1


Frozen v1.0beta1 22269e3
help Creators and Submitter
Creators
Submitter
Tools
gfastats
seqtk
Minimap2
DeepTools
License
MIT License
Activity

Views: 290   Downloads: 75   Runs: 0

Created: 29th Mar 2025 at 03:01

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