Assembly-Hifi-only-VGP3/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
  2. Haplotype 2 assembly
  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 assemblie

SEEK ID: https://workflowhub.eu/workflows/612?version=4

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?
Genomescope Summary Genomescope Summary n/a
  • File
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
7 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.7+galaxy0
8 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0
9 Pick parameter value pick_value
10 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
11 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy0
12 Hifiasm toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1
13 Convert Convert characters1
14 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
15 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
16 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
17 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
18 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
19 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
20 Cut Cut1
21 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0
22 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3
23 Data Prep Primary n/a
24 Data Prep Alternate n/a
25 Estimated genome size param_value_from_file
26 Plotting Nx and Sizes n/a
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 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0
30 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0
31 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0

Outputs

ID Name Description Type
cutadapt multiqc stats cutadapt multiqc stats n/a
  • File
multiqc html report multiqc html report n/a
  • File
Hifiasm Primary gfa Hifiasm Primary gfa n/a
  • File
Hifiasm Alternate gfa Hifiasm Alternate gfa n/a
  • File
Usable GFA Primary Usable GFA Primary n/a
  • File
Usable GFA Alternate Usable GFA Alternate n/a
  • File
Hifiasm Primary assembly Hifiasm Primary assembly n/a
  • File
Hifiasm Alternate assembly Hifiasm Alternate assembly n/a
  • File
Busco summary image Busco summary image n/a
  • File
Merqury png Merqury png n/a
  • File
Merqury completeness stats Merqury completeness stats n/a
  • File
Merqury Histograms Merqury Histograms n/a
  • File
Estimated Genome size Estimated Genome size n/a
  • File
Size Plot Size Plot n/a
  • File
Nx Plot Nx Plot 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
Assembly statistics Assembly statistics n/a
  • File

Version History

v0.2.1 (latest) Created 7th Oct 2024 at 16:34 by WorkflowHub Bot

Updated to v0.2.1


Frozen v0.2.1 1262df6

v0.2 Created 3rd Aug 2024 at 03:01 by WorkflowHub Bot

Updated to v0.2


Frozen v0.2 173b906

v0.1.8 Created 24th Jul 2024 at 03:02 by WorkflowHub Bot

Updated to v0.1.8


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v0.1.7 Created 18th Jul 2024 at 03:02 by WorkflowHub Bot

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v0.1.6 Created 10th Jul 2024 at 03:02 by WorkflowHub Bot

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v0.1.5 Created 30th Apr 2024 at 03:01 by WorkflowHub Bot

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v0.1.4 Created 23rd Apr 2024 at 03:02 by WorkflowHub Bot

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v0.1.3 Created 27th Mar 2024 at 03:02 by WorkflowHub Bot

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Frozen v0.1.3 9bf277d

v0.1.2 Created 13th Jan 2024 at 03:01 by WorkflowHub Bot

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v0.1.1 Created 24th Nov 2023 at 03:02 by WorkflowHub Bot

Updated to v0.1.1


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v0.1 (earliest) Created 20th Oct 2023 at 03:01 by WorkflowHub Bot

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Frozen v0.1 1f63570
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: 5405   Downloads: 1343   Runs: 1

Created: 20th Oct 2023 at 03:01

Last updated: 17th Aug 2024 at 03:02

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