Assembly-Hifi-only-VGP3/main

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Workflow Type: Galaxy

Generate a genome assembly based on PacBio HiFi reads. Part of the VGP suite, it needs to be run after the VGP1 k-mer profiling workflow. The assembly contigs are built using HiFiasm, and the workflow generates assembly statistics, BUSCO reports, Merqury plots, and the contigs in fasta and GFA formats.

SEEK ID: https://workflowhub.eu/workflows/612?version=21

Inputs

ID Name Description Type
Assembly Name Assembly Name For workflow report.
  • string
Bits for Hifiasm bloom filter Bits for Hifiasm 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
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
Meryl Database Meryl Database n/a
  • File
Name of alternate assembly Name of alternate assembly n/a
  • string?
Name of primary assembly Name of primary assembly n/a
  • string?
Pacbio Reads Collection Pacbio Reads Collection n/a
  • File[]
Species Name Species Name For workflow report.
  • string

Steps

ID Name Description
12 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
13 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
14 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.0+galaxy0
15 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+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 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
19 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3
20 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy0
21 Cut Cut1
22 Convert Convert characters1
23 Parse parameter value param_value_from_file
24 Cut Cut1
25 Homozygous read coverage for Hifiasm toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
26 Estimated genome size param_value_from_file
27 Hifiasm toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.25.0+galaxy0
28 Raw Unitig Image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
29 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
30 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
31 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
32 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
33 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
34 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
35 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
36 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
37 gfastats 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 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1
40 compleasm toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy2
41 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4
42 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0
43 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0
44 Data Prep Primary n/a
45 Data Prep Alternate n/a
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 merqury_stats __EXTRACT_DATASET__
51 Join two Datasets join1
52 Plotting Nx and Sizes n/a
53 Advanced Cut toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy0
54 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0

Outputs

ID Name Description Type
Species Name for report Species Name for report n/a
  • File
Assembly Name for report Assembly Name for report n/a
  • File
Lineage for report Lineage for report 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
Hifiasm Primary gfa Hifiasm Primary gfa n/a
  • File
Hifiasm Alternate gfa Hifiasm Alternate gfa n/a
  • File
raw unitig graph image raw unitig graph image n/a
  • File
Usable GFA Primary Usable GFA Primary n/a
  • File
Usable GFA Primary no sequences Usable GFA Primary no sequences n/a
  • File
Usable GFA Alternate Usable GFA Alternate n/a
  • File
Usable GFA Alternate no sequences Usable GFA Alternate no sequences n/a
  • File
Hifiasm Primary assembly Hifiasm Primary assembly n/a
  • File
Hifiasm Alternate assembly Hifiasm Alternate assembly n/a
  • File
Assembly Stats on Primary assembly Assembly Stats on Primary assembly n/a
  • File
Assembly Stats on Alternate Assembly Assembly Stats on Alternate Assembly n/a
  • File
Busco summary image Busco summary image n/a
  • File
Busco Summary Busco Summary n/a
  • File
Compleasm on Primary Assembly contigs: Miniprot Compleasm on Primary Assembly contigs: Miniprot n/a
  • File
Compleasm on Primary Assembly contigs: Translated Proteins Compleasm on Primary Assembly contigs: Translated Proteins n/a
  • File
Compleasm on Primary Assembly contigs: Full table Busco Compleasm on Primary Assembly contigs: Full table Busco n/a
  • File
Compleasm on Primary Assembly contigs: Full table Compleasm on Primary Assembly contigs: Full table n/a
  • File
Merqury png Merqury png n/a
  • File
Merqury Histograms Merqury Histograms n/a
  • File
Merqury completeness stats Merqury completeness stats 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
merqury_stats merqury_stats n/a
  • File
Nx Plot Nx Plot n/a
  • File
Size Plot Size Plot n/a
  • File
Assembly statistics Assembly statistics 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
BUSCO
Merqury
Bandage
compleasm
License
Creative Commons Attribution 4.0 International
Activity

Views: 10408   Downloads: 3165   Runs: 16

Created: 20th Oct 2023 at 03:01

Last updated: 16th May 2025 at 03:02

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