TSI-Scaffolding-with-HiC (based on VGP-HiC-scaffolding)
Version 1

Workflow Type: Galaxy

Scaffolding using HiC data with YAHS

This workflow has been created from a Vertebrate Genomes Project (VGP) scaffolding workflow.

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.


  • 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


ID Name Description Type
Estimated genome size in bp Estimated genome size in bp n/a
  • int
HiC Forward reads HiC Forward reads Forward reads as a single dataset in fastq format
  • File
HiC reverse reads HiC reverse reads Reverse reads as a single dataset in fastq format
  • 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
assembly.fasta assembly.fasta n/a
  • File


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__


ID Name Description Type
YAHS on input dataset(s): Final scaffolds agp output YAHS on input dataset(s): Final scaffolds agp output n/a
  • File
Reconciliated Scaffolds: gfa Reconciliated Scaffolds: gfa n/a
  • File
Scaffold sizes for s2 Scaffold sizes for s2 n/a
  • File
Reconciliated Scaffolds: fasta Reconciliated Scaffolds: fasta n/a
  • File
Assembly Statistics for s2 Assembly Statistics for s2 n/a
  • File
Pretext Map Before HiC scaffolding Pretext Map Before HiC scaffolding n/a
  • File
Busco Summary Busco Summary n/a
  • File
Busco Summary image Busco Summary image 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

Version 1 (earliest) Created 21st Jun 2024 at 01:48 by Anna Syme

Initial commit

Frozen Version-1 75c60cd
help Creators and Submitter
  • VGP Project
Additional credit

VGP, Galaxy

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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