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=11

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?
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
HiC forward reads HiC forward reads Forward reads as a single dataset in fastq format
  • File
HiC reverse reads HiC reverse reads Reverse reads as a single dataset in fastq format
  • 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 n/a
  • string?
Name for Haplotype 2 Name for Haplotype 2 n/a
  • string?
Pacbio Reads Collection Pacbio Reads Collection A simple list containing PacBio data in either fasta or fastq formats.
  • File[]
SAK input file SAK input file n/a
  • File?

Steps

ID Name Description
12 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1
13 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1
14 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0
15 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
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 Estimated homozygous read coverage 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/1.3.6+galaxy0
26 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
27 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
28 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
29 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
30 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
31 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
32 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
33 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
34 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
35 Data Prep Hap2 n/a
36 Data Prep Hap1 n/a
37 Text transformation toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1
38 Text transformation toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1
39 Join two Datasets join1
40 Plot Data n/a
41 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0
42 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4
43 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0
44 Advanced Cut toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1
45 output_merqury.spectra-cn.fl __EXTRACT_DATASET__
46 output_merqury.spectra-asm.fl __EXTRACT_DATASET__
47 merqury_qv __EXTRACT_DATASET__
48 output_merqury.assembly_01.spectra-cn.fl __EXTRACT_DATASET__
49 merqury_stats __EXTRACT_DATASET__
50 output_merqury.assembly_02.spectra-cn.fl __EXTRACT_DATASET__
51 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1

Outputs

ID Name Description Type
Cutadapt on input dataset(s): Read 1 Output Cutadapt on input dataset(s): Read 1 Output n/a
  • File
Estimated Genome size Estimated Genome size n/a
  • File
raw unitig graph image raw unitig graph image n/a
  • File
usable hap2 gfa usable hap2 gfa n/a
  • File
usable hap1 gfa usable hap1 gfa n/a
  • File
Hifiasm HiC hap2 Hifiasm HiC hap2 n/a
  • File
Hifiasm HiC hap1 Hifiasm HiC hap1 n/a
  • File
Size Plot Size Plot n/a
  • File
Nx Plot Nx Plot n/a
  • File
Busco Summary Image Hap2 Busco Summary Image Hap2 n/a
  • File
Busco Summary Hap2 Busco Summary Hap2 n/a
  • File
Busco Gff File - Hap2 Busco Gff File - Hap2 n/a
  • File
Merqury images Merqury images n/a
  • File
Merqury Histograms Merqury Histograms n/a
  • File
Merqury QV Merqury QV n/a
  • File
Merqury Stats Merqury Stats n/a
  • File
Busco Summary Image Hap1 Busco Summary Image Hap1 n/a
  • File
Busco Gff File - Hap1 Busco Gff File - Hap1 n/a
  • File
Busco Summary Hap1 Busco Summary 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: 5327   Downloads: 1275   Runs: 0

Created: 4th Nov 2023 at 03:01

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