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=9

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 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
10 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1
11 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1
12 Pick parameter value toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
13 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0
14 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
15 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1
16 Cut Cut1
17 Convert Convert characters1
18 Parse parameter value param_value_from_file
19 Cut Cut1
20 Homozygous read coverage for Hifiasm toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
21 Estimated genome size param_value_from_file
22 Hifiasm toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0
23 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
24 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
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 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0
32 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4
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 Primary n/a
36 Data Prep Alternate n/a
37 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1
38 Plotting Nx and Sizes n/a

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
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 image Busco summary image n/a
  • File
Merqury png Merqury png n/a
  • File
Merqury Histograms Merqury Histograms n/a
  • File
Merqury completeness stats Merqury completeness stats n/a
  • File
Assembly statistics Assembly statistics n/a
  • File
Nx Plot Nx Plot n/a
  • File
Size Plot Size Plot 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


Frozen v0.1.8 f991481

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

Updated to v0.1.7


Frozen v0.1.7 3dd5731

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

Updated to v0.1.6


Frozen v0.1.6 8d8c799

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

Updated to v0.1.5


Frozen v0.1.5 e57076e

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

Updated to v0.1.4


Frozen v0.1.4 262adb5

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

Updated to v0.1.3


Frozen v0.1.3 9bf277d

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

Updated to v0.1.2


Frozen v0.1.2 acbbe2c

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

Updated to v0.1.1


Frozen v0.1.1 544422d

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

Updated to v0.1


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: 5067   Downloads: 1258   Runs: 1

Created: 20th Oct 2023 at 03:01

Last updated: 17th Aug 2024 at 03:02

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