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

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 n/a
  • File
Genomescope Summary Genomescope Summary n/a
  • File
HiC forward reads HiC forward reads n/a
  • File
HiC reverse reads HiC reverse reads n/a
  • File
Lineage Lineage n/a
  • string
Meryl Database Meryl Database n/a
  • 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 n/a
  • File[]
SAK input file SAK input file n/a
  • File?

Steps

ID Name Description
11 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1
12 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0
13 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
14 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
15 Cut Cut1
16 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2
17 Estimated homozygous read coverage param_value_from_file
18 Convert Convert characters1
19 Hifiasm toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.16.1+galaxy4
20 Cut Cut1
21 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
22 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+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 Raw Unitig Image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
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 Estimated genome size param_value_from_file
29 Text transformation toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1
30 Text transformation toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1
31 gfastats_data_prep n/a
32 gfastats_data_prep n/a
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 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.3.2+galaxy0
36 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2
37 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.3.2+galaxy0
38 gfastats_plot n/a
39 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2
40 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2
41 Cut Cut1
42 Paste Paste1

Outputs

ID Name Description Type
Cutadapt on input dataset(s): Read 1 Output Cutadapt on input dataset(s): Read 1 Output n/a
  • File
usable hap1 gfa usable hap1 gfa n/a
  • File
usable hap2 gfa usable hap2 gfa n/a
  • File
Estimated Genome size Estimated Genome size n/a
  • File
Hifiasm HiC hap1 Hifiasm HiC hap1 n/a
  • File
Hifiasm HiC hap2 Hifiasm HiC hap2 n/a
  • File
Busco Summary Hap1 Busco Summary Hap1 n/a
  • File
Busco Summary Image Hap1 Busco Summary Image Hap1 n/a
  • File
Merqury images Merqury images n/a
  • File
Busco Summary Image Hap2 Busco Summary Image Hap2 n/a
  • File
Busco Summary Hap2 Busco Summary Hap2 n/a
  • File
Nx Plot Nx Plot n/a
  • File
Size Plot Size Plot n/a
  • File
Assembly statistics fir Hap1 and Hap2 Assembly statistics fir Hap1 and Hap2 n/a
  • File

Version History

v0.1.3 (latest) Created 3rd Oct 2024 at 03:05 by WorkflowHub Bot

Updated to v0.1.3


Frozen v0.1.3 e076662

v0.2.2 Created 13th Aug 2024 at 03:02 by WorkflowHub Bot

Updated to v0.2.2


Frozen v0.2.2 d7114a9

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: 4663   Downloads: 1102   Runs: 0

Created: 4th Nov 2023 at 03:01

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