Workflow Type: Galaxy

Assembly with Hifi reads and Trio Data

Generate phased assembly based on PacBio Hifi Reads using parental Illumina data for phasing

Inputs

  1. Hifi long reads [fastq]
  2. Concatenated Illumina reads : Paternal [fastq]
  3. Concatenated Illumina reads : Maternal [fastq]
  4. K-mer database [meryldb]
  5. Paternal hapmer database [meryldb]
  6. Maternal hapmer database [meryldb]
  7. Genome profile summary generated by Genomescope [txt]
  8. Genome model parameters generated by Genomescope [tabular]
  9. Homozygous read coverage (Estimated from the Genomescope model if not provided)
  10. Lineage of the species being assembled
  11. Bloom Filter
  12. Name of first haplotype
  13. Name of second haplotype

Outputs

  1. Haplotype 1 assembly
  2. Haplotype 2 assembly
  3. QC: BUSCO report for both assemblies
  4. Merqury report for both assemblies
  5. Assembly statistics for both assemblies
  6. Nx Plot for both assemblies
  7. Size plot for both assemblies

Steps

ID Name Description
16 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1
17 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0
18 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1
19 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
20 Cut Cut1
21 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1
22 Parse parameter value param_value_from_file
23 Convert Convert characters1
24 Homozygous read coverage for Hifiasm toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
25 Cut Cut1
26 Hifiasm toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0
27 Estimated genome size param_value_from_file
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 Raw Unitig Image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
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 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
34 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
35 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
36 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
37 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0
38 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0
39 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4
40 Data prep Hap1 n/a
41 Data Prep Hap2 n/a
42 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
43 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
44 merqury_qv __EXTRACT_DATASET__
45 output_merqury.spectra-cn.fl __EXTRACT_DATASET__
46 output_merqury.spectra-asm.fl __EXTRACT_DATASET__
47 output_merqury.assembly_01.spectra-cn.fl __EXTRACT_DATASET__
48 output_merqury.assembly_02.spectra-cn.fl __EXTRACT_DATASET__
49 merqury_stats __EXTRACT_DATASET__
50 Plots n/a
51 Join two Datasets join1
52 Advanced Cut toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1
53 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1

Version History

v0.2 (latest) Created 7th Oct 2024 at 16:34 by WorkflowHub Bot

Updated to v0.2


Frozen v0.2 8429b3e

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

Updated to v0.1.8


Frozen v0.1.8 9a11432

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

Updated to v0.1.7


Frozen v0.1.7 18ebec0

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

Updated to v0.1.6


Frozen v0.1.6 55a88b1

v0.1.4 Created 30th May 2024 at 11:36 by WorkflowHub Bot

Updated to v0.1.4


Frozen v0.1.4 b639087

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

Updated to v0.1.3


Frozen v0.1.3 a2195cc

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

Updated to v0.1.2


Frozen v0.1.2 80829a9

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

Updated to v0.1.1


Frozen v0.1.1 056ec76

v0.1 (earliest) Created 4th Nov 2023 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 21959c8
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Views: 4541   Downloads: 1002   Runs: 0

Created: 4th Nov 2023 at 03:01

Last updated: 17th Aug 2024 at 03:02

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