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

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 Summary Genomescope Summary n/a
  • File
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
7 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0
8 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
9 Pick parameter value pick_value
10 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
11 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2
12 Hifiasm toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy0
13 Convert Convert characters1
14 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
15 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
16 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
17 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
18 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
19 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
20 Cut Cut1
21 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0
22 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3
23 gfastats_data_prep n/a
24 gfastats_data_prep n/a
25 Estimated genome size param_value_from_file
26 gfastats_plot n/a
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 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2
30 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2
31 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2

Outputs

ID Name Description Type
multiqc html report multiqc html report n/a
  • File
cutadapt multiqc stats cutadapt multiqc stats n/a
  • File
Hifiasm Primary gfa Hifiasm Primary gfa n/a
  • File
Hifiasm Alternate gfa Hifiasm Alternate gfa n/a
  • File
Usable GFA Primary Usable GFA Primary n/a
  • File
Usable GFA Alternate Usable GFA Alternate n/a
  • File
Hifiasm Primary assembly Hifiasm Primary assembly n/a
  • File
Hifiasm Alternate assembly Hifiasm Alternate assembly n/a
  • File
Busco summary image Busco summary image n/a
  • File
Merqury completeness stats Merqury completeness stats n/a
  • File
Merqury png Merqury png n/a
  • File
Estimated Genome size Estimated Genome size n/a
  • File
Nx Plot Nx Plot n/a
  • File
Size Plot Size Plot 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
Assembly statistics Assembly statistics n/a
  • File

Version History

v0.1.2 (latest) 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
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Galaxy, VGP

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Views: 870

Created: 20th Oct 2023 at 03:01

Last updated: 13th Jan 2024 at 03:01

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