Workflows

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146 Workflows visible to you, out of a total of 146
nf-core/methylseq

GitHub Actions CI Status GitHub Actions Linting StatusAWS CI[![Cite ...

Type: Nextflow

Creator: Phil Ewels

Submitter: WorkflowHub Bot

Assembly-Hifi-Trio-phasing-VGP5/main

Assembly with Hifi reads and Trio Data

Generate phased assembly based on PacBio Hifi Reads using parental Illumina data for phasing

Inputs

  1. Hifi long reads [fastq]
  2. Concatenated Illumina reads : Paternal [fastq]
  3. Concatenated Illumina reads : Maternal [fastq]
  4. K-mer database [meryldb]
  5. Paternal hapmer database [meryldb]
  6. Maternal hapmer database [meryldb]
  7. Genome profile summary generated by Genomescope [txt]
  8. Genome model parameters generated by Genomescope [tabular]

...

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

kmer-profiling-hifi-VGP1/main

VGP Workflow #1

This workflow produces a Meryl database and Genomescope outputs that will be used to determine parameters for following workflows, and assess the quality of genome assemblies. Specifically, 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.

Inputs

  • A collection of Hifi long reads in FASTQ format
  • k-mer length
  • Ploidy

Outputs

  • Meryl Database of kmer counts

...

Type: Galaxy

Creator: VGP, Galaxy

Submitter: WorkflowHub Bot

kmer-profiling-hifi-trio-VGP2/main

Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury. Part of the VGP pipeline.

Type: Galaxy

Creator: VGP, Galaxy

Submitter: WorkflowHub Bot

nf-core/phaseimpute

Phasing and imputation pipeline

Type: Nextflow

Creators: Louis Le Nezet, Anabella Trigila

Submitter: WorkflowHub Bot

clinicalmp-discovery/main

Workflow for clinical metaproteomics database searching

Type: Galaxy

Creator: Subina Mehta

Submitter: WorkflowHub Bot

Assembly-Hifi-only-VGP3/main

Contiging Solo:

Generate assembly based on PacBio Hifi Reads.

Inputs

  1. Hifi long reads [fastq]
  2. K-mer database [meryldb]
  3. Genome profile summary generated by Genomescope [txt]
  4. Homozygous Read Coverage. Optional, use if you think the estimation from Genomescope is inacurate.
  5. Genomescope Model Parameters generated by Genomescope [tabular]
  6. Database for busco lineage (recommended: latest)
  7. Busco lineage (recommended: vertebrata)
  8. Name of first assembly
  9. Name of second ...

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

clinicalmp-data-interpretation/main

This workflow will perform taxonomic and functional annotations using Unipept and statistical analysis using MSstatsTMT.

Type: Galaxy

Creator: GalaxyP

Submitter: WorkflowHub Bot

clinicalmp-verification/main

In proteomics research, verifying detected peptides is essential for ensuring data accuracy and biological relevance. This tutorial continues from the clinical metaproteomics discovery workflow, focusing on verifying identified microbial peptides using the PepQuery tool.

Type: Galaxy

Creator: Pratik Jagtap

Submitter: WorkflowHub Bot

nf-core/metapep

From metagenomes to peptides

Type: Nextflow

Creators: Sabrina Krakau, Leon Kuchenbecker and Till Englert

Submitter: WorkflowHub Bot

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