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. Genome model parameters generated by Genomescope [tabular]
  9. Homozygous read coverage (Estimated from the Genomescope model if not provided)
  10. Lineage of the species being assembled
  11. Bloom Filter
  12. Name of first haplotype
  13. 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=11

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?
Database for Busco Lineage Database for Busco Lineage n/a
  • string
Genomescope Model Parameters Genomescope Model Parameters GenomeScope model parameters generated by K-mer profiling workflow
  • File
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
Homozygous Read Coverage Homozygous Read Coverage If empty, read coverage will be estimated from the Genomescope parameters.
  • int?
Lineage Lineage Taxonomic lineage for the organism being assembled for Busco analysis
  • string
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?
Utilize homology information to correct trio-phasing errors Utilize homology information to correct trio-phasing errors --trio-dual option
  • boolean?

Steps

ID Name Description
16 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1
17 Pick parameter value toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
18 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1
19 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1
20 Pick parameter value toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
21 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0
22 Cut Cut1
23 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1
24 Parse parameter value param_value_from_file
25 Convert Convert characters1
26 Homozygous read coverage for Hifiasm toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
27 Cut Cut1
28 Hifiasm toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.20.0+galaxy0
29 Estimated genome size param_value_from_file
30 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1
31 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1
32 Raw Unitig Image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
33 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1
34 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1
35 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1
36 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1
37 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1
38 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1
39 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0
40 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0
41 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4
42 Data prep Hap1 n/a
43 Data Prep Hap2 n/a
44 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
45 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
46 merqury_qv __EXTRACT_DATASET__
47 output_merqury.spectra-cn.fl __EXTRACT_DATASET__
48 output_merqury.spectra-asm.fl __EXTRACT_DATASET__
49 output_merqury.assembly_01.spectra-cn.fl __EXTRACT_DATASET__
50 output_merqury.assembly_02.spectra-cn.fl __EXTRACT_DATASET__
51 merqury_stats __EXTRACT_DATASET__
52 Plots n/a
53 Join two Datasets join1
54 Advanced Cut toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2
55 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1

Outputs

ID Name Description Type
json_stats json_stats n/a
  • File
multiqc html report multiqc html report n/a
  • File
cutadapt multiqc stats cutadapt multiqc stats n/a
  • File
Estimated Genome size Estimated Genome size n/a
  • File
usable hap1 gfa usable hap1 gfa n/a
  • File
usable hap2 gfa usable hap2 gfa n/a
  • File
raw unitig graph image raw unitig graph image n/a
  • File
Hifiasm Trio hap1 Hifiasm Trio hap1 n/a
  • File
Hifiasm Trio hap2 Hifiasm Trio hap2 n/a
  • File
Busco Gff Hap1 Busco Gff Hap1 n/a
  • File
Busco Summary Hap1 Busco Summary Hap1 n/a
  • File
Busco Summary Image Hap1 Busco Summary Image 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 Images Merqury Images n/a
  • File
Merqury QV Merqury QV n/a
  • File
Merqury Trio Histogram Merqury Trio Histogram n/a
  • File
merqury_qv merqury_qv n/a
  • File
output_merqury.spectra-cn.fl output_merqury.spectra-cn.fl n/a
  • File
output_merqury.spectra-asm.fl output_merqury.spectra-asm.fl n/a
  • File
output_merqury.assembly_01.spectra-cn.fl output_merqury.assembly_01.spectra-cn.fl n/a
  • File
output_merqury.assembly_02.spectra-cn.fl output_merqury.assembly_02.spectra-cn.fl n/a
  • File
merqury_stats merqury_stats n/a
  • File
Nx Plot Nx Plot n/a
  • File
Size Plot Size Plot n/a
  • File
Assembly statistics for Hap1 and Hap2 Assembly statistics for Hap1 and Hap2 n/a
  • File
clean_stats clean_stats n/a
  • File

Version History

v0.4 (latest) Created 17th Dec 2024 at 03:02 by WorkflowHub Bot

Updated to v0.4


Frozen v0.4 59b1d83

v0.3 Created 4th Dec 2024 at 03:02 by WorkflowHub Bot

Updated to v0.3


Frozen v0.3 071efe1

v0.2 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: 5624   Downloads: 1255   Runs: 0

Created: 4th Nov 2023 at 03:01

Last updated: 17th Dec 2024 at 03:02

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