Assembly-Hifi-Trio-phasing-VGP5/main

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Workflow Type: Galaxy

Genome Assembly with Hifi reads and Trio Data

Generate phased assembly based on PacBio Hifi Reads using parental Illumina data for phasing. Part of the VGP workflow suite, it needs to be run after the Trio k-mer Profiling workflow VGP2.

Inputs

  1. Hifi long reads [fastq]
  2. Concatenated Illumina reads : Paternal [fastq]
  3. Concatenated Illumina reads : Maternal [fastq]
  4. K-mer database [meryldb] generated by VGP2 workflow.
  5. Paternal hapmer database [meryldb] generated by VGP2 workflow.
  6. Maternal hapmer database [meryldb] generated by VGP2 workflow.
  7. Bits for Bloom Filter. Change for large genomes to save memory.
  8. Database to use for Busco lineages. Recommended : latest version.
  9. Lineage. Select the taxonomic lineage of the assembled species.
  10. Homozygous read coverage (Estimated from the Genomescope model if not provided)
  11. Genome model parameters generated by Genomescope [tabular] generated by VGP2 workflow.
  12. Genome profile summary generated by Genomescope [txt] generated by VGP2 workflow.
  13. Name of first haplotype
  14. Name of second haplotype

Outputs

  1. Haplotype 1 assembly [fasta] and [gfa]
  2. Haplotype 2 assembly [fasta] and [gfa]
  3. QC: Size plot for both assemblies
  4. QC: MultiQC report for HiFi reads trimming
  5. QC: BUSCO report for both assemblies
  6. QC: Merqury report for both assemblies
  7. QC: Assembly statistics for both assemblies
  8. QC: Nx plot for both assemblies
  9. QC: Size plot for both assemblies

SEEK ID: https://workflowhub.eu/workflows/642?version=18

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[]
Utilize homology information to correct trio-phasing errors Utilize homology information to correct trio-phasing errors --trio-dual option
  • boolean?

Steps

ID Name Description
15 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.0+galaxy0
16 Pick parameter value toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
17 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1
18 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy0
19 Pick parameter value toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
20 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3
21 Cut Cut1
22 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy0
23 Parse parameter value param_value_from_file
24 Convert Convert characters1
25 Homozygous read coverage for Hifiasm toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
26 Cut Cut1
27 Hifiasm toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.24.0+galaxy0
28 Estimated genome size param_value_from_file
29 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
30 No Sequence hap2 gfa toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
31 Raw Unitig Image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
32 No Sequence hap1 gfa toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
33 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
34 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
35 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
36 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
37 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
38 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
39 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
40 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0
41 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0
42 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4
43 Data prep Hap1 n/a
44 Data Prep Hap2 n/a
45 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0
46 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0
47 merqury_qv __EXTRACT_DATASET__
48 output_merqury.spectra-cn.fl __EXTRACT_DATASET__
49 output_merqury.spectra-asm.fl __EXTRACT_DATASET__
50 output_merqury.assembly_01.spectra-cn.fl __EXTRACT_DATASET__
51 output_merqury.assembly_02.spectra-cn.fl __EXTRACT_DATASET__
52 merqury_stats __EXTRACT_DATASET__
53 Plots n/a
54 Join two Datasets join1
55 Advanced Cut toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy0
56 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0

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
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 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 Summary Hap2 Busco Summary Hap2 n/a
  • File
Busco Gff Hap2 Busco Gff 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

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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: 8089   Downloads: 2157   Runs: 1

Created: 4th Nov 2023 at 03:01

Last updated: 26th Mar 2025 at 12:01

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