Workflow Type: Galaxy

Scaffolding with Bionano

Scaffolding using Bionano optical map data

Inputs

  1. Bionano data [cmap]
  2. Estimated genome size [txt]
  3. Phased assembly generated by Hifiasm [gfa1]

Outputs

  1. Scaffolds
  2. Non-scaffolded contigs
  3. QC: Assembly statistics
  4. QC: Nx plot
  5. QC: Size plot

Inputs

ID Name Description Type
Bionano Data Bionano Data n/a
  • File
Conflict resolution files Conflict resolution files n/a
  • File?
Estimated genome size - Parameter File Estimated genome size - Parameter File n/a
  • File
Input GFA Input GFA n/a
  • File

Steps

ID Name Description
4 Parse parameter value param_value_from_file
5 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
6 Bionano Hybrid Scaffold toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy3
7 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
8 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
9 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
10 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
11 gfastats_data_prep n/a
12 Cut Cut1
13 Cut Cut1
14 Scatterplot with ggplot2 toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1
15 Scatterplot with ggplot2 toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1

Outputs

ID Name Description Type
Scaffolds: agp Scaffolds: agp n/a
  • File
Bionano scaffolds reconciliated: gfa Bionano scaffolds reconciliated: gfa n/a
  • File
Bionano scaffolds reconciliated: fasta Bionano scaffolds reconciliated: fasta n/a
  • File
Assembly Statistics for s1 Assembly Statistics for s1 n/a
  • File
Nx Plot Nx Plot n/a
  • File
Size Plot Size Plot n/a
  • File

Version History

v0.1.3 (latest) Created 23rd Apr 2024 at 03:02 by WorkflowHub Bot

Updated to v0.1.3


Frozen v0.1.3 36cb074

v0.1.2 Created 7th Mar 2024 at 03:02 by WorkflowHub Bot

Updated to v0.1.2


Frozen v0.1.2 e583530

v0.1.1 Created 16th Nov 2023 at 03:01 by WorkflowHub Bot

Updated to v0.1.1


Frozen v0.1.1 e2301a3

v0.1 (earliest) Created 4th Nov 2023 at 03:02 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 cdcc509
help Creators and Submitter
Creators
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Additional credit

Galaxy, VGP

Submitter
Activity

Views: 2402   Downloads: 435

Created: 4th Nov 2023 at 03:02

Last updated: 23rd Apr 2024 at 03:02

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