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

Steps

ID Name Description
12 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.7+galaxy0
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/0.19.8+galaxy1
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 Cut Cut1
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 Paste Paste1

Version History

v0.2.2 (latest) Created 7th Oct 2024 at 16:34 by WorkflowHub Bot

Updated to v0.2.2


Frozen v0.2.2 d7114a9

v0.1.3 Created 7th Oct 2024 at 16:34 by WorkflowHub Bot

Updated to v0.1.3


Frozen v0.1.3 e076662

v0.2.1 Created 1st Aug 2024 at 03:02 by WorkflowHub Bot

Updated to v0.2.1


Frozen v0.2.1 910e7e9

v0.2 Created 25th Jul 2024 at 03:02 by WorkflowHub Bot

Updated to v0.2


Frozen v0.2 072818f

v0.1.11 Created 10th Jul 2024 at 03:02 by WorkflowHub Bot

Updated to v0.1.11


Frozen v0.1.11 56e4920

v0.1.10 Created 30th Apr 2024 at 03:02 by WorkflowHub Bot

Updated to v0.1.10


Frozen v0.1.10 e9bd8c7

v0.1.9 Created 23rd Apr 2024 at 03:02 by WorkflowHub Bot

Updated to v0.1.9


Frozen v0.1.9 98cb786

v0.1.8 Created 27th Mar 2024 at 03:02 by WorkflowHub Bot

Updated to v0.1.8


Frozen v0.1.8 364f983

v0.1.7 Created 24th Nov 2023 at 03:02 by WorkflowHub Bot

Updated to v0.1.7


Frozen v0.1.7 ba11d4e

v0.1.6 Created 17th Nov 2023 at 03:01 by WorkflowHub Bot

Updated to v0.1.6


Frozen v0.1.6 a4ae5bd

v0.1.4 Created 9th Nov 2023 at 03:01 by WorkflowHub Bot

Updated to v0.1.4


Frozen v0.1.4 284d0df

v0.1.2 Created 8th Nov 2023 at 03:02 by WorkflowHub Bot

Updated to v0.1.2


Frozen v0.1.2 341bbdf

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

Updated to v0.1


Frozen v0.1 ac570c9
help Creators and Submitter
Creator
  • Delphine Lariviere
Additional credit

Galaxy, VGP

Submitter
Activity

Views: 5791   Downloads: 1419   Runs: 0

Created: 4th Nov 2023 at 03:01

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