Assembly-Hifi-Trio-phasing-VGP5/main

View on GitHub Download RO-Crate Run on Galaxy
Workflow Type: Galaxy

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=4

Inputs

ID Name Description Type
Bits for bloom filter Bits for bloom filter Defaults to 37 if not specified. For genomes much larger than human, applying -f38 or even -f39 is preferred to save memory on k-mer counting.
  • int?
Genomescope Summary Genomescope Summary n/a
  • File
Hapmer Database : Maternal Hapmer Database : Maternal n/a
  • File
Hapmer Database : Paternal Hapmer Database : Paternal n/a
  • File
Maternal Illumina reads (hap2) Maternal Illumina reads (hap2) n/a
  • File[]
Meryl Database : Child Meryl Database : Child n/a
  • File
Name for Haplotype 1 Name for Haplotype 1 n/a
  • string?
Name for Haplotype 2 Name for Haplotype 2 n/a
  • string?
Pacbio Reads Collection : child Pacbio Reads Collection : child n/a
  • File[]
Paternal Illumina reads (hap1) Paternal Illumina reads (hap1) n/a
  • File[]
SAK input file (Optional) SAK input file (Optional) n/a
  • File?

Steps

ID Name Description
11 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.7+galaxy0
12 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0
13 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
14 Hifiasm toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1
15 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy0
16 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
17 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
18 Raw Unitig Image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
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 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
23 Convert Convert characters1
24 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0
25 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0
26 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3
27 Data prep Hap1 n/a
28 Data Prep Hap2 n/a
29 Cut Cut1
30 Plots n/a
31 Estimated genome size param_value_from_file
32 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
33 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
34 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0
35 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0
36 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0

Outputs

ID Name Description Type
json_stats json_stats n/a
  • File
cutadapt multiqc stats cutadapt multiqc stats n/a
  • File
multiqc html report multiqc html report n/a
  • File
usable hap1 gfa usable hap1 gfa n/a
  • File
usable hap2 gfa usable hap2 gfa n/a
  • File
Hifiasm Trio hap1 Hifiasm Trio hap1 n/a
  • File
Hifiasm Trio hap2 Hifiasm Trio hap2 n/a
  • File
Busco Summary Image Hap1 Busco Summary Image Hap1 n/a
  • File
Busco Summary Hap1 Busco Summary Hap1 n/a
  • File
Busco Gff Hap1 Busco Gff Hap1 n/a
  • File
Busco Gff Hap2 Busco Gff Hap2 n/a
  • File
Busco Summary Hap2 Busco Summary Hap2 n/a
  • File
Busco Summary Image Hap2 Busco Summary Image Hap2 n/a
  • File
Merqury Trio Histogram Merqury Trio Histogram n/a
  • File
Merqury Images Merqury Images n/a
  • File
Nx Plot Nx Plot n/a
  • File
Size Plot Size Plot n/a
  • File
Estimated Genome size Estimated Genome size n/a
  • File
Assembly statistics for Hap1 and Hap2 Assembly statistics for Hap1 and Hap2 n/a
  • File

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: 4940   Downloads: 1073   Runs: 0

Created: 4th Nov 2023 at 03:01

Last updated: 17th Aug 2024 at 03:02

help Tags

This item has not yet been tagged.

help Attributions

None

Total size: 149 KB
Powered by
 (v.1.16.0-main)
About WorkflowHub | Acknowledgements | Credits | Terms & Conditions | Privacy Policy | Cite us | Contact us
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH