Assembly-Hifi-Trio-phasing-VGP5/main

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Assembly with Hifi reads and Trio Data

Generate phased assembly based on PacBio Hifi Reads using parental Illumina data for phasing

Inputs

  1. Hifi long reads [fastq]
  2. Concatenated Illumina reads : Paternal [fastq]
  3. Concatenated Illumina reads : Maternal [fastq]
  4. K-mer database [meryldb]
  5. Paternal hapmer database [meryldb]
  6. Maternal hapmer database [meryldb]
  7. Genome profile summary generated by Genomescope [txt]
  8. Bloom Filter
  9. Name of first haplotype
  10. Name of second haplotype

Outputs

  1. Haplotype 1 assembly
  2. Haplotype 2 assembly
  3. QC: BUSCO report for both assemblies
  4. Merqury report for both assemblies
  5. Assembly statistics for both assemblies
  6. Nx Plot for both assemblies
  7. Size plot for both assemblies

SEEK ID: https://workflowhub.eu/workflows/642?version=3

Steps

ID Name Description
11 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0
12 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
13 Hifiasm toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy0
14 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2
15 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
16 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
17 Raw Unitig Image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
18 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
19 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
20 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
21 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
22 Convert Convert characters1
23 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0
24 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0
25 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3
26 gfastats_data_prep n/a
27 gfastats_data_prep n/a
28 Cut Cut1
29 gfastats_plot n/a
30 Estimated genome size param_value_from_file
31 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
32 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
33 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2
34 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2
35 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2

Version History

v0.2 (latest) Created 7th Oct 2024 at 16:34 by WorkflowHub Bot

Updated to v0.2


Frozen v0.2 8429b3e

v0.1.8 Created 24th Jul 2024 at 03:02 by WorkflowHub Bot

Updated to v0.1.8


Frozen v0.1.8 9a11432

v0.1.7 Created 18th Jul 2024 at 03:02 by WorkflowHub Bot

Updated to v0.1.7


Frozen v0.1.7 18ebec0

v0.1.6 Created 10th Jul 2024 at 03:02 by WorkflowHub Bot

Updated to v0.1.6


Frozen v0.1.6 55a88b1

v0.1.4 Created 30th May 2024 at 11:36 by WorkflowHub Bot

Updated to v0.1.4


Frozen v0.1.4 b639087

v0.1.3 Created 27th Mar 2024 at 03:02 by WorkflowHub Bot

Updated to v0.1.3


Frozen v0.1.3 a2195cc

v0.1.2 Created 13th Jan 2024 at 03:01 by WorkflowHub Bot

Updated to v0.1.2


Frozen v0.1.2 80829a9

v0.1.1 Created 24th Nov 2023 at 03:02 by WorkflowHub Bot

Updated to v0.1.1


Frozen v0.1.1 056ec76

v0.1 (earliest) Created 4th Nov 2023 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 21959c8
help Creators and Submitter
Creators
Not specified
Additional credit

Galaxy, VGP

Submitter
Tools
Cutadapt
MultiQC
gfastats
Bandage
BUSCO
Merqury
License
Creative Commons Attribution 4.0 International
Activity

Views: 4936   Downloads: 1073   Runs: 0

Created: 4th Nov 2023 at 03:01

Last updated: 17th Aug 2024 at 03:02

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