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
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

VGP-meryldb-creation-trio/main
Version 1

VGP Workflow #1

Inputs

Outputs

Inputs

Steps

Outputs

Version History

v0.1 (earliest) Created 14th Jun 2022 at 03:01 by WorkflowHub Bot

Creators

Submitter

VGP-meryldb-creation-trio/main Version 1

VGP Workflow #1

Inputs

Outputs

Inputs

Steps

Outputs

Version History

v0.1 (earliest) Created 14th Jun 2022 at 03:01 by WorkflowHub Bot

Creators

Submitter

Related items

VGP-meryldb-creation-trio/main
Version 1