Assembly-Hifi-HiC-phasing-VGP4/main

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Workflow Type: Galaxy

Assemble Genome using PacBio HiFi and HiC data from the same individual for phasing. Prerequisite: Run k-mer profiling workflow (VGP1). This workflow uses HiFiasm for contigging, and generates assembly statistics, BUSCO reports, Merqury histograms, and the genome assembly contigs in fasta and GFA format.

SEEK ID: https://workflowhub.eu/workflows/641?version=20

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 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 - Forward Hi-C reads - Forward n/a
  • File[]
Hi-C reads - Reverse Hi-C reads - Reverse 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[]
SAK input file SAK input file Do not use.
  • File?
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 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.0+galaxy0
15 Sort Forward __SORTLIST__
16 Sort Reverse __SORTLIST__
17 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy0
18 Pick parameter value toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
19 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1
20 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3
21 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.0+galaxy0
22 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy0
23 Cut Cut1
24 Pick forward toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
25 Pick reverse toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
26 Convert Convert characters1
27 Estimated homozygous read coverage param_value_from_file
28 Collapse forward reads toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
29 Collapse reverse reads toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
30 Cut Cut1
31 Homozygous read coverage for Hifiasm toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
32 Estimated genome size param_value_from_file
33 Hifiasm toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.25.0+galaxy0
34 Raw Unitig Image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
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 gfa hap2 no sequences 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 gfastats gfa hap1 toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
41 gfastats gfa hap2 toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
42 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
43 gfastats gfa hap1 no sequences toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
44 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
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 Data Prep Hap2 n/a
48 Data Prep Hap1 n/a
49 Text transformation toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy0
50 Text transformation toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy0
51 Join two Datasets join1
52 Plot Data n/a
53 Busco Hap2 toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1
54 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4
55 Busco Hap1 toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1
56 Advanced Cut toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy0
57 output_merqury.spectra-cn.fl __EXTRACT_DATASET__
58 output_merqury.spectra-asm.fl __EXTRACT_DATASET__
59 merqury_qv __EXTRACT_DATASET__
60 output_merqury.assembly_01.spectra-cn.fl __EXTRACT_DATASET__
61 merqury_stats __EXTRACT_DATASET__
62 output_merqury.assembly_02.spectra-cn.fl __EXTRACT_DATASET__
63 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0

Outputs

ID Name Description Type
Cutadapt on input dataset(s): Read 1 Output Cutadapt on input dataset(s): Read 1 Output n/a
  • File
Clean Hi-C forward reads Clean Hi-C forward reads n/a
  • File
Clean Hi-C reverse reads Clean Hi-C reverse 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
Size Plot Size Plot n/a
  • File
Nx Plot Nx Plot n/a
  • File
Busco Summary Hap2 Busco Summary Hap2 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
Merqury Histograms Merqury Histograms n/a
  • File
Merqury QV Merqury QV n/a
  • File
Merqury Stats Merqury Stats n/a
  • File
Merqury images Merqury images 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
Assembly statistics for Hap1 and Hap2 Assembly statistics for Hap1 and Hap2 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
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
Activity

Views: 10410   Downloads: 3131   Runs: 0

Created: 4th Nov 2023 at 03:01

Last updated: 26th Mar 2025 at 10:06

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