Assembly-Hifi-HiC-phasing-VGP4/main

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Workflow Type: Galaxy

Contiging Solo w/HiC:

Generate phased assembly based on PacBio Hifi Reads using HiC data from the same individual for phasing.

Inputs

  1. Hifi long reads [fastq]
  2. HiC forward reads (if multiple input files, concatenated in same order as reverse reads) [fastq]
  3. HiC reverse reads (if multiple input files, concatenated in same order as forward reads) [fastq]
  4. K-mer database [meryldb]
  5. Genome profile summary generated by Genomescope [txt]
  6. Name of first assembly
  7. Name of second assembly

Outputs

  1. Haplotype 1 assembly ([fasta] and [gfa])
  2. Haplotype 2 assembly ([fasta] and [gfa])
  3. QC: BUSCO report for both assemblies
  4. QC: Merqury report for both assemblies
  5. QC: Assembly statistics for both assemblies
  6. QC: Nx plot for both assemblies
  7. QC: Size plot for both assemblies

SEEK ID: https://workflowhub.eu/workflows/641?version=25

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 Select the database to use for Busco lineages.
  • string
Genomescope Model Parameters Genomescope Model Parameters GenomeScope model parameters generated by K-mer profiling workflow
  • File
Genomescope Summary Genomescope Summary GenomeScope summary generated by K-mer profiling workflow
  • File
Hi-C reads Hi-C reads 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 Meryl database generated by K-mer profiling workflow
  • File
Name for Haplotype 1 Name for Haplotype 1 Name of the first haplotype without blank space.
  • string?
Name for Haplotype 2 Name for Haplotype 2 Name of the second haplotype without blank space.
  • string?
Pacbio Reads Pacbio Reads A simple list containing PacBio data in either fasta or fastq formats.
  • File[]
Species Name Species Name For workflow report.
  • string
Trim Hi-C reads? Trim Hi-C reads? Trim 5 bases at the beginning of each read. Use with Arima Hi-C data if the Hi-C map looks "noisy".
  • boolean

Steps

ID Name Description
14 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
15 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
16 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.1+galaxy0
17 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.1+galaxy0
18 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy2
19 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
20 Pick parameter value toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
21 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1
22 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3
23 Pick forward 2 toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
24 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy2
25 Cut Cut1
26 Filter empty datasets __FILTER_EMPTY_DATASETS__
27 Convert Convert characters1
28 Estimated homozygous read coverage param_value_from_file
29 Unzip collection __UNZIP_COLLECTION__
30 Cut Cut1
31 Homozygous read coverage for Hifiasm toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
32 Collapse forward reads toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
33 Collapse reverse reads toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
34 Estimated genome size param_value_from_file
35 Hifiasm toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.25.0+galaxy0
36 Raw Unitig Image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
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 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
40 gfastats gfa hap2 no sequences 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 gfa hap1 toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
43 gfastats gfa hap2 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 gfastats gfa hap1 no sequences toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
46 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
47 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2
48 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2
49 Data Prep Hap2 n/a
50 Data Prep Hap1 n/a
51 Text transformation toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy2
52 Text transformation toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy2
53 Join two Datasets join1
54 Plot Data n/a
55 Busco Hap2 toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1
56 Compleasm Hap2 toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy2
57 Busco Hap1 toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1
58 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4
59 Compleasm Hap1 toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy2
60 Advanced Cut toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy2
61 output_merqury.spectra-cn.fl __EXTRACT_DATASET__
62 output_merqury.spectra-asm.fl __EXTRACT_DATASET__
63 merqury_qv __EXTRACT_DATASET__
64 output_merqury.assembly_01.spectra-cn.fl __EXTRACT_DATASET__
65 merqury_stats __EXTRACT_DATASET__
66 output_merqury.assembly_02.spectra-cn.fl __EXTRACT_DATASET__
67 Unique lines toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.5+galaxy2
68 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2

Outputs

ID Name Description Type
Species Name for workflow report Species Name for workflow report n/a
  • File
Assembly Name for workflow report Assembly Name for workflow report n/a
  • File
Cutadapt on input dataset(s): Read 1 Output Cutadapt on input dataset(s): Read 1 Output n/a
  • File
Lineage for workflow report Lineage for workflow report n/a
  • File
Clean Hi-C reads Clean Hi-C reads n/a
  • File
Estimated Genome size Estimated Genome size n/a
  • File
raw unitig graph image raw unitig graph image n/a
  • File
No Sequences hap2 gfa No Sequences hap2 gfa n/a
  • File
usable hap1 gfa usable hap1 gfa n/a
  • File
usable hap2 gfa usable hap2 gfa n/a
  • File
No sequences hap1 gfa No sequences hap1 gfa n/a
  • File
Hifiasm Hi-C hap2 Hifiasm Hi-C hap2 n/a
  • File
Hifiasm Hi-C hap1 Hifiasm Hi-C hap1 n/a
  • File
Nx Plot Nx Plot n/a
  • File
Size Plot Size Plot n/a
  • File
Busco Gff File - Hap2 Busco Gff File - Hap2 n/a
  • File
Busco Summary Image Hap2 Busco Summary Image Hap2 n/a
  • File
Busco Summary Hap2 Busco Summary Hap2 n/a
  • File
Compleasm on Contigs hap2 Miniprot Compleasm on Contigs hap2 Miniprot n/a
  • File
Compleasm hap2 Full Table Busco Compleasm hap2 Full Table Busco n/a
  • File
Compleasm on Contigs hap2 Full Table Compleasm on Contigs hap2 Full Table n/a
  • File
Compleasm on Contigs hap2 Translated Proteins Compleasm on Contigs hap2 Translated Proteins n/a
  • File
Busco Gff File - Hap1 Busco Gff File - Hap1 n/a
  • File
Busco Summary Hap1 Busco Summary Hap1 n/a
  • File
Busco Summary Image Hap1 Busco Summary Image Hap1 n/a
  • File
Merqury images Merqury images n/a
  • File
Merqury Histograms Merqury Histograms n/a
  • File
Merqury Stats Merqury Stats n/a
  • File
Merqury QV Merqury QV n/a
  • File
Compleasm on Contigs hap1 Translated Proteins Compleasm on Contigs hap1 Translated Proteins n/a
  • File
Compleasm on Contigs hap1 Miniprot Compleasm on Contigs hap1 Miniprot n/a
  • File
Compleasm on Contigs hap1 Full Table Compleasm on Contigs hap1 Full Table n/a
  • File
Compleasm on Contigs hap1 Full Table Busco Compleasm on Contigs hap1 Full Table Busco 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
merqury_qv merqury_qv 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
output_merqury.assembly_02.spectra-cn.fl output_merqury.assembly_02.spectra-cn.fl 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
Creator
  • Delphine Lariviere
Additional credit

Galaxy, VGP

Submitter
License
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Activity

Views: 24264   Downloads: 125168   Runs: 0

Created: 4th Nov 2023 at 03:01

Last updated: 26th Mar 2025 at 10:06

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