Workflows

What is a Workflow?
170 Workflows visible to you, out of a total of 170
influenza-isolates-consensus-and-subtyping/main

This workflow performs subtyping and consensus sequence generation for batches of Illumina PE sequenced Influenza A isolates.

Type: Galaxy

Creators: Wolfgang Maier, Viktoria Isabel Schwarz

Submitter: WorkflowHub Bot

nf-core/nanostring

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Type: Nextflow

Creators: Peltzer , Alexander & Mohr, Christopher

Submitter: WorkflowHub Bot

scanpy-clustering/main

Single-cell RNA-seq workflow with Scanpy and Anndata. Based on the 3k PBMC clustering tutorial from Scanpy. It takes count matrix, barcodes and feature files as input and creates an Anndata object out of them. It then performs QC and filters for lowly expressed genes and cells. Then the data is normalized and scaled. Then PCs are computed to further cluster using louvain algorithm. It also generated various plots of clustering colored with highly ranked genes.

Type: Galaxy

Creators: Pavankumar Videm, Hans-Rudolf Hotz, Mehmet Tekman, Bérénice Batut

Submitter: WorkflowHub Bot

annotation-helixer/main

This workflow allows you to annotate a genome with Helixer and evaluate the quality of the annotation using BUSCO and Genome Annotation statistics. GFFRead is also used to predict protein sequences derived from this annotation, and BUSCO and OMArk are used to assess proteome quality.

Type: Galaxy

Creator: Romane Libouban

Submitter: WorkflowHub Bot

nf-core/pixelator

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Type: Nextflow

Creator: Pixelgen Technologies AB

Submitter: WorkflowHub Bot

nf-core/rangeland

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Type: Nextflow

Creators: None

Submitter: WorkflowHub Bot

nf-core/references

help community build references

Type: Nextflow

Creator: @maxulysse

Submitter: WorkflowHub Bot

nf-core/methylseq

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Type: Nextflow

Creator: Phil Ewels

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

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