This workflow does not specify a "main" workflow file.
Workflow Type: Galaxy
VGP Workflow #1
This workflow collects the metrics on the properties of the genome under consideration by analyzing the k-mer frequencies. It provides information about the genomic complexity, such as the genome size and levels of heterozygosity and repeat content, as well about the data quality. It uses reads from two parental genomes to partition long reads from the offspring into haplotype-specific k-mer databases.
Inputs
- Collection of Hifi long reads in FASTQ format
- Paternal short-read Illumina sequencing reads in FASTQ format
- Maternal short-read Illumina sequencing reads in FASTQ format
Outputs
- Meryl databases of k-mer counts
- Child
- Paternal haplotype
- Maternal haplotype
- GenomeScope metrics of child and parental genomes
- Linear plot
- Log plot
- Transformed linear plot
- Transformed log plot
- Summary
- Model
- Model parameteres
Inputs
ID | Name | Description | Type |
---|---|---|---|
K-mer length | K-mer length | K-mer length used to calculate k-mer spectra. For a human genome, the best k-mer size is k=21 for both haploid (3.1G) or diploid (6.2G). | n/a |
Pacbio Hifi reads | Pacbio Hifi reads | n/a | n/a |
Collection of Paired Reads - Paternal | Collection of Paired Reads - Paternal | Collection of Paired Illumina Data in fastq format for Parent 1. | n/a |
Collection of Paired Reads - Maternal | Collection of Paired Reads - Maternal | Collection of Paired Illumina Data in fastq format for Parent 2. | n/a |
Ploidy | Ploidy | Ploidy for model to use. Default=2 | n/a |
operation_type | operation_type | runtime parameter for tool Meryl | n/a |
operation_type | operation_type | runtime parameter for tool Meryl | n/a |
operation_type | operation_type | runtime parameter for tool Meryl | n/a |
input | input | runtime parameter for tool GenomeScope | n/a |
input | input | runtime parameter for tool GenomeScope | n/a |
input | input | runtime parameter for tool GenomeScope | n/a |
Steps
ID | Name | Description |
---|---|---|
0 | K-mer length | K-mer length used to calculate k-mer spectra. For a human genome, the best k-mer size is k=21 for both haploid (3.1G) or diploid (6.2G). |
1 | Pacbio Hifi reads | |
2 | Collection of Paired Reads - Paternal | Collection of Paired Illumina Data in fastq format for Parent 1. |
3 | Collection of Paired Reads - Maternal | Collection of Paired Illumina Data in fastq format for Parent 2. |
4 | Ploidy | Ploidy for model to use. Default=2 |
5 | FASTQ interlacer | toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0 |
6 | FASTQ interlacer | toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0 |
7 | Meryl | toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6 |
8 | Meryl | toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6 |
9 | Meryl | toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6 |
10 | Meryl | toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6 |
11 | GenomeScope | toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy1 |
12 | Meryl | toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6 |
13 | Meryl | toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6 |
14 | Meryl | toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6 |
15 | Genomescope on paternal haplotype | toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy1 |
16 | Genomescope on maternal haplotype | toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy1 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
outfile_pairs_from_coll | outfile_pairs_from_coll | n/a | |
outfile_singles_from_coll | outfile_singles_from_coll | n/a | |
outfile_pairs_from_coll | outfile_pairs_from_coll | n/a | |
outfile_singles_from_coll | outfile_singles_from_coll | n/a | |
read_db | read_db | n/a | |
read_db | read_db | n/a | |
read_db_hist | read_db_hist | n/a | |
pat_db | pat_db | n/a | |
pat_db_hist | pat_db_hist | n/a | |
mat_db | mat_db | n/a | |
mat_db_hist | mat_db_hist | n/a | |
read_db | read_db | n/a | |
read_db | read_db | n/a | |
linear_plot | linear_plot | n/a | |
log_plot | log_plot | n/a | |
transformed_linear_plot | transformed_linear_plot | n/a | |
transformed_log_plot | transformed_log_plot | n/a | |
model | model | n/a | |
summary | summary | n/a | |
read_db | read_db | n/a | |
read_db_hist | read_db_hist | n/a | |
read_db_hist | read_db_hist | n/a | |
linear_plot | linear_plot | n/a | |
log_plot | log_plot | n/a | |
transformed_linear_plot | transformed_linear_plot | n/a | |
transformed_log_plot | transformed_log_plot | n/a | |
model | model | n/a | |
summary | summary | n/a | |
linear_plot | linear_plot | n/a | |
log_plot | log_plot | n/a | |
transformed_linear_plot | transformed_linear_plot | n/a | |
transformed_log_plot | transformed_log_plot | n/a | |
model | model | n/a | |
summary | summary | n/a |
Version History
v0.1 (earliest) Created 14th Jun 2022 at 03:01 by WorkflowHub Bot
Updated to v0.1
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v0.1
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Created: 14th Jun 2022 at 03:01
Last used: 25th Jun 2022 at 19:32

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