Assembly-Hifi-only-VGP3/main

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Workflow Type: Galaxy

Contiging Solo:

Generate assembly based on PacBio Hifi Reads.

Inputs

  1. Hifi long reads [fastq]
  2. K-mer database [meryldb]
  3. Genome profile summary generated by Genomescope [txt]
  4. Homozygous Read Coverage. Optional, use if you think the estimation from Genomescope is inacurate.
  5. Genomescope Model Parameters generated by Genomescope [tabular]
  6. Database for busco lineage (recommended: latest)
  7. Busco lineage (recommended: vertebrata)
  8. Name of first assembly
  9. Name of second assembly

Outputs

  1. Primary assembly
  2. Alternate assembly
  3. QC: Bandage image for the raw unitigs
  4. QC: BUSCO report for both assemblies
  5. QC: Merqury report for both assemblies
  6. QC: Assembly statistics for both assemblies
  7. QC: Nx plot for both assemblies
  8. QC: Size plot for both assemblie

SEEK ID: https://workflowhub.eu/workflows/612?version=12

Inputs

ID Name Description Type
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[]
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/4.9+galaxy1
12 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1
13 Pick parameter value toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
14 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1
15 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0
16 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1
17 Cut Cut1
18 Convert Convert characters1
19 Parse parameter value param_value_from_file
20 Cut Cut1
21 Homozygous read coverage for Hifiasm toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
22 Estimated genome size param_value_from_file
23 Hifiasm toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0
24 Raw Unitig Image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
25 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0
26 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0
27 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0
28 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0
29 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0
30 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0
31 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0
32 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0
33 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0
34 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4
35 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
36 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
37 Data Prep Primary n/a
38 Data Prep Alternate n/a
39 merqury_qv __EXTRACT_DATASET__
40 output_merqury.spectra-cn.fl __EXTRACT_DATASET__
41 output_merqury.spectra-asm.fl __EXTRACT_DATASET__
42 output_merqury.assembly_01.spectra-cn.fl __EXTRACT_DATASET__
43 merqury_stats __EXTRACT_DATASET__
44 Join two Datasets join1
45 Plotting Nx and Sizes n/a
46 Advanced Cut toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2
47 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1

Outputs

ID Name Description Type
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 Alternate gfa Hifiasm Alternate gfa n/a
  • File
Hifiasm Primary gfa Hifiasm Primary gfa n/a
  • File
raw unitig graph image raw unitig graph image n/a
  • File
Usable GFA Alternate Usable GFA Alternate n/a
  • File
Usable GFA Primary Usable GFA Primary 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 Busco Summary n/a
  • File
Busco summary image Busco summary image n/a
  • File
Merqury completeness stats Merqury completeness stats n/a
  • File
Merqury png Merqury png n/a
  • File
Merqury Histograms Merqury Histograms 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
Size Plot Size Plot n/a
  • File
Nx Plot Nx Plot n/a
  • File
Assembly statistics Assembly statistics n/a
  • File
clean_stats clean_stats n/a
  • File

Version History

v0.2.2 (latest) Created 4th Dec 2024 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
BUSCO
Merqury
Bandage
License
Creative Commons Attribution 4.0 International
Activity

Views: 6178   Downloads: 1596   Runs: 1

Created: 20th Oct 2023 at 03:01

Last updated: 4th Dec 2024 at 03:02

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