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 GenomeScope model parameters generated by K-mer profiling workflow
  • File
Genomescope Summary Genomescope Summary GenomeScope summary generated by K-mer profiling workflow
  • File
HiC forward reads HiC forward reads Forward reads as a single dataset in fastq format
  • File
HiC reverse reads HiC reverse reads Reverse reads as a single dataset in fastq format
  • File
Lineage Lineage Taxonomic lineage for the organism being assembled for Busco analysis
  • string
Meryl Database Meryl Database Meryl database generated by K-mer profiling workflow
  • 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 A simple list containing PacBio data in either fasta or fastq formats.
  • 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/4.4+galaxy0
12 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
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/1.1.2
16 Cut Cut1
17 Convert Convert characters1
18 Estimated homozygous read coverage param_value_from_file
19 Cut Cut1
20 Hifiasm toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy0
21 Estimated genome size param_value_from_file
22 Raw Unitig Image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
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 gfastats_data_prep n/a
32 gfastats_data_prep n/a
33 Text transformation toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1
34 Text transformation toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1
35 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2
36 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2
37 gfastats_plot n/a
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+galaxy3
40 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0
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
Estimated Genome size Estimated Genome size n/a
  • File
usable hap2 gfa usable hap2 gfa n/a
  • File
usable hap1 gfa usable hap1 gfa n/a
  • File
Hifiasm HiC hap2 Hifiasm HiC hap2 n/a
  • File
Hifiasm HiC hap1 Hifiasm HiC hap1 n/a
  • File
Size Plot Size Plot n/a
  • File
Nx Plot Nx Plot n/a
  • File
Busco Summary Image Hap2 Busco Summary Image Hap2 n/a
  • File
Busco Summary Hap2 Busco Summary Hap2 n/a
  • File
Merqury images Merqury images n/a
  • File
Busco Summary Hap1 Busco Summary Hap1 n/a
  • File
Busco Summary Image Hap1 Busco Summary Image Hap1 n/a
  • File
Assembly statistics fir Hap1 and Hap2 Assembly statistics fir Hap1 and Hap2 n/a
  • File

Version History

v0.1.7 (latest) 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: 923

Created: 4th Nov 2023 at 03:01

help Tags
help Attributions

None

Total size: 154 KB
Powered by
(v.1.14.1)
Copyright © 2008 - 2023 The University of Manchester and HITS gGmbH