Assembly-Hifi-Trio-phasing-VGP5/main

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Workflow Type: Galaxy

Generate phased assembly based on PacBio HiFi reads and parental Illumina data for phasing. Part of the VGP workflow suite, it needs to be run after the Trio k-mer Profiling workflow VGP2. This workflow uses HiFiasm for contigging, and generates assembly statistics, BUSCO reports, Merqury plots, and the genome assembly contigs in fasta and GFA format.

SEEK ID: https://workflowhub.eu/workflows/642?version=21

Inputs

ID Name Description Type
Assembly Name Assembly Name For workflow report.
  • string
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[]
Species Name Species Name For workflow report.
  • string
Utilize homology information to correct trio-phasing errors Utilize homology information to correct trio-phasing errors --trio-dual option
  • boolean?

Steps

ID Name Description
17 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
18 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
19 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.0+galaxy0
20 Pick parameter value toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
21 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
22 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1
23 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy0
24 Pick parameter value toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
25 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3
26 Cut Cut1
27 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy0
28 Parse parameter value param_value_from_file
29 Convert Convert characters1
30 Homozygous read coverage for Hifiasm toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
31 Cut Cut1
32 Hifiasm toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.25.0+galaxy0
33 Estimated genome size param_value_from_file
34 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
35 No Sequence hap2 gfa toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
36 Raw Unitig Image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
37 No Sequence hap1 gfa toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
38 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
39 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
40 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
41 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
42 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
43 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
44 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
45 Busco Hap1 toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1
46 Compleasm Hap1 toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy2
47 Busco Hap2 toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1
48 Compleasm Hap2 toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy2
49 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4
50 Data prep Hap1 n/a
51 Data Prep Hap2 n/a
52 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0
53 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0
54 merqury_qv __EXTRACT_DATASET__
55 output_merqury.spectra-cn.fl __EXTRACT_DATASET__
56 output_merqury.spectra-asm.fl __EXTRACT_DATASET__
57 output_merqury.assembly_01.spectra-cn.fl __EXTRACT_DATASET__
58 output_merqury.assembly_02.spectra-cn.fl __EXTRACT_DATASET__
59 merqury_stats __EXTRACT_DATASET__
60 Plots n/a
61 Join two Datasets join1
62 Advanced Cut toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy0
63 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0

Outputs

ID Name Description Type
Species for report Species for report n/a
  • File
Assembly for report Assembly for report n/a
  • File
json_stats json_stats n/a
  • File
Lineage for report Lineage for report n/a
  • File
cutadapt multiqc stats cutadapt multiqc stats n/a
  • File
multiqc html report multiqc html report n/a
  • File
Estimated Genome size Estimated Genome size n/a
  • File
usable hap1 gfa usable hap1 gfa n/a
  • File
No Sequence hap2 gfa No Sequence hap2 gfa n/a
  • File
raw unitig graph image raw unitig graph image n/a
  • File
No Sequence hap1 gfa No Sequence 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 Hap1 Busco Summary Hap1 n/a
  • File
Busco Gff Hap1 Busco Gff Hap1 n/a
  • File
Busco Summary Image Hap1 Busco Summary Image Hap1 n/a
  • File
Compleasm on Hap1 (paternal) contigs: Full table Compleasm on Hap1 (paternal) contigs: Full table n/a
  • File
Compleasm on Hap1 (paternal) contigs: Full table Busco Compleasm on Hap1 (paternal) contigs: Full table Busco n/a
  • File
Compleasm on Hap1 (paternal) contigs: Miniprot Compleasm on Hap1 (paternal) contigs: Miniprot n/a
  • File
Compleasm on Hap1 (paternal) contigs: Translated Proteins Compleasm on Hap1 (paternal) contigs: Translated Proteins 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
Compleasm on Hap2 (maternal) contigs: Full table Compleasm on Hap2 (maternal) contigs: Full table n/a
  • File
Compleasm on Hap2 (maternal) contigs: Miniprot Compleasm on Hap2 (maternal) contigs: Miniprot n/a
  • File
Compleasm on Hap2 (maternal) contigs: Translated Proteins Compleasm on Hap2 (maternal) contigs: Translated Proteins n/a
  • File
Compleasm on Hap2 (maternal) contigs: Full table Busco Compleasm on Hap2 (maternal) contigs: Full table Busco 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

v0.9.5 (latest) Created 16th May 2025 at 03:02 by WorkflowHub Bot

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help Creators and Submitter
Creators
Not specified
Additional credit

Galaxy, VGP

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

Views: 9897   Downloads: 2903   Runs: 1

Created: 4th Nov 2023 at 03:01

Last updated: 16th May 2025 at 03:02

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