Workflow Type: Galaxy

This workflow perform the scaffolding of a genome assemble using HiC data with YAHS. Part of the VGP set of workflows.

Inputs

ID Name Description Type
Database for Busco Lineage Database for Busco Lineage Select the database to use for Busco lineage.
  • string
Estimated genome size - Parameter File Estimated genome size - Parameter File Estimated genome size from contiging workflow.
  • File
Haplotype Haplotype Select the haplotype being scaffolded.
  • string
Hi-C reads Hi-C reads n/a
  • File[]
Input GFA Input GFA The input GFA must conform to gfa1.2 standards, i.e. should have 'P' lines defined, and contain sequences. Output GFAs from assemblers can be run through a GFA-GFA conversion using gfastats to ensure this.
  • File
Lineage Lineage Taxonomic lineage for the organism being assembled for Busco analysis.
  • string
Restriction enzymes Restriction enzymes Restriction enzymes used in preparation of Hi-C libraries.
  • string
SAK input file SAK input file Do not use.
  • File?
Sequence graph Sequence graph Provide AGP for Scaffolding.
  • File?
Trim Hi-C Data? Trim 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". (Select No if you are using the trimmed data generated by a previous workflow)
  • boolean

Steps

ID Name Description
10 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
11 Parse parameter value param_value_from_file
12 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
13 Trim and Align Hi-C paired collection n/a
14 YAHS toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy2
15 PretextMap toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1
16 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0
17 Pretext Snapshot toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0
18 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
19 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
20 Extract dataset __EXTRACT_DATASET__
21 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
22 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
23 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
24 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy3
25 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0
26 gfastats_data_prep n/a
27 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0
28 Samtools merge toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2
29 Cut Cut1
30 Cut Cut1
31 bedtools BAM to BED toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0
32 PretextMap toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1
33 Nx Plot toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1
34 Size Plot toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1
35 Sort toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.5+galaxy0
36 Pretext Snapshot toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0
37 Extract dataset __EXTRACT_DATASET__

Outputs

ID Name Description Type
s1 Merged Hi-C Alignments s1 Merged Hi-C Alignments n/a
  • File
s1 Trimmed Hi-C data s1 Trimmed Hi-C data n/a
  • File
s1 Hi-C Alignments s1 Hi-C Alignments n/a
  • File
YAHS on input dataset(s): Final scaffolds agp output YAHS on input dataset(s): Final scaffolds agp output n/a
  • File
Reconciliated Scaffolds: gfa no sequence Reconciliated Scaffolds: gfa no sequence n/a
  • File
Reconciliated Scaffolds: gfa Reconciliated Scaffolds: gfa n/a
  • File
Pretext Map Before HiC scaffolding Pretext Map Before HiC scaffolding n/a
  • File
Reconciliated Scaffolds: fasta Reconciliated Scaffolds: fasta n/a
  • File
Scaffold sizes for s2 Scaffold sizes for s2 n/a
  • File
Assembly Statistics for s2 Assembly Statistics for s2 n/a
  • File
Hi-C Alignments Hi-C Alignments n/a
  • File
Busco Summary Busco Summary n/a
  • File
Busco Summary image Busco Summary image n/a
  • File
clean_stats clean_stats n/a
  • File
s2 Merged Hi-C Alignments s2 Merged Hi-C Alignments n/a
  • File
Nx Plot Nx Plot n/a
  • File
Size Plot Size Plot n/a
  • File
Pretext Map After HiC scaffolding Pretext Map After HiC scaffolding n/a
  • File

Version History

v1.3 (latest) Created 29th Mar 2025 at 03:02 by WorkflowHub Bot

Updated to v1.3


Frozen v1.3 6ac1ca9

v1.2 Created 26th Mar 2025 at 12:00 by WorkflowHub Bot

Updated to v1.2


Frozen v1.2 13406fa

v1.1 Created 26th Mar 2025 at 12:00 by WorkflowHub Bot

Updated to v1.1


Frozen v1.1 42b038b

v1.0 Created 26th Mar 2025 at 12:00 by WorkflowHub Bot

Updated to v1.0


Frozen v1.0 ff48f3e

v0.3 Created 5th Feb 2025 at 03:02 by WorkflowHub Bot

Updated to v0.3


Frozen v0.3 60a248b

v0.2.8 Created 7th Oct 2024 at 16:33 by WorkflowHub Bot

Updated to v0.2.8


Frozen v0.2.8 53e128f

v0.2.7 Created 7th Oct 2024 at 16:33 by WorkflowHub Bot

Updated to v0.2.7


Frozen v0.2.7 5accfa6

v0.2.6 Created 7th Oct 2024 at 16:33 by WorkflowHub Bot

Updated to v0.2.6


Frozen v0.2.6 8b4b766

v0.2.5 Created 1st Aug 2024 at 03:01 by WorkflowHub Bot

Updated to v0.2.5


Frozen v0.2.5 f76e5c5

v0.2.4 Created 30th May 2024 at 11:35 by WorkflowHub Bot

Updated to v0.2.4


Frozen v0.2.4 03dd848

v0.2.3 Created 24th Apr 2024 at 03:01 by WorkflowHub Bot

Updated to v0.2.3


Frozen v0.2.3 7479a72

v0.2.2 Created 27th Mar 2024 at 03:02 by WorkflowHub Bot

Updated to v0.2.2


Frozen v0.2.2 8b8fe66

v0.2.1 Created 24th Nov 2023 at 03:02 by WorkflowHub Bot

Updated to v0.2.1


Frozen v0.2.1 faa9803

v0.2 Created 17th Nov 2023 at 03:02 by WorkflowHub Bot

Updated to v0.2


Frozen v0.2 b9afa62

v0.1.2 Created 16th Nov 2023 at 03:02 by WorkflowHub Bot

Updated to v0.1.2


Frozen v0.1.2 81d58fc

v0.1.1 Created 31st Oct 2023 at 03:02 by WorkflowHub Bot

Updated to v0.1.1


Frozen v0.1.1 bde67a2

v0.1 (earliest) Created 27th Oct 2023 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 95a269d
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Views: 9182   Downloads: 2514   Runs: 1

Created: 27th Oct 2023 at 03:01

Last updated: 29th Mar 2025 at 03:02

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