Workflows

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850 Workflows visible to you, out of a total of 931
ERGA Long reads-only Assembly+QC Hifiasm v2505 (WF2)
Stable

The workflow takes a long reads collection (HiFi, or ONT also possible now), and max coverage depth (calculated from WF1) to run Hifiasm in solo mode. It produces a Pri/Alt assembly, Bandage plots, and runs all the QC analysis (gfastats, BUSCO, and Merqury).

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

DOI: 10.48546/workflowhub.workflow.1162.1

SeuratExtend

SeuratExtend: An Enhanced Toolkit for scRNA-seq Analysis

Overview

SeuratExtend is an R package designed to provide an improved and easy-to-use toolkit for scRNA-seq analysis and visualization, built upon the Seurat object. While Seurat is a widely-used tool in the R community that offers a foundational framework for scRNA-seq analysis, it has limitations when it comes to more advanced analysis and customized visualization. SeuratExtend expands upon Seurat by offering an array of ...

Type: Unrecognized workflow type

Creator: Yichao Hua

Submitter: Yichao Hua

DOI: 10.48546/workflowhub.workflow.1385.1

kmer-profiling-hifi-VGP1/main

Evaluation of Pacbio Hifi Reads and genome profiling. 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

Matrix Multiplication - improved resources visualization

Application that perform the multiplication between matrices.

Type: COMPSs

Creator: Raül Sirvent

Submitter: Nicolò Giacomini

nf-core/multiplesequencealign

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

Type: Nextflow

Creators: Luisa Santus, Jose Espinosa Carrasco

Submitter: WorkflowHub Bot

lcms-preprocessing/main

This workflow is composed with the XCMS tool R package (Smith, C.A. 2006) able to extract, filter, align and fill gapand the possibility to annotate isotopes, adducts and fragments using the CAMERA R package (Kuhl, C 2012).

https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html

Type: Galaxy

Creator: workflow4metabolomics

Submitter: WorkflowHub Bot

Scaffolding-HiC-VGP8/main

This workflow performs the scaffolding of a genome assembly using HiC data with YAHS. Can be used on any assembly with Hi-C data, and the assembly in the gfa format. You can generate a gfa from a fasta using the gfastat tool. Part of the VGP set of workflows, it is meant to be run after the contigging (workflows 3,4, or 5), optional purging step (Workflow 6 or 6b), and an optionnal scaffolding with Bionano data (Workflow 7). This workflow includes QC with Assembly statistics, Busco, and Hi-C maps. ...

Type: Galaxy

Creator: VGP, Galaxy

Submitter: WorkflowHub Bot

Mitogenome-assembly-VGP0/main

Generate mitochondrial assembly based on PacBio HiFi reads. Part of the VGP suite, it can be run at any time independently of the other workflows. This workflow uses MitoHiFi and a mitochondrial reference to assemble the mitochondrial genome from PacBio reads. You do not need to provide the reference yourself, only the Latin name of the species.

Type: Galaxy

Creator: VGP, Galaxy

Submitter: WorkflowHub Bot

Pure COMPSs Kmeans with Provenance Run

K-means COMPSs application

Type: COMPSs

Creator: Rosa M Badia

Submitter: Panna Lukacs

Gene Fetch
Stable

Gene_fetch

This tool fetches gene sequences from NCBI databases based on taxonomy IDs (taxids) or taxonomic information. It can retrieve both protein and nucleotide sequences for various genes, including protein-coding genes (e.g., cox1, cytb, rbcl, matk) and rRNA genes (e.g., 16S, 18S).

Feature highlight

  • Fetch protein and/or nucleotide sequences from NCBI GenBank database.
  • Handles both direct nucleotide sequences and protein-linked nucleotide searches (CDS extraction includes fallback ...

Type: Python

Creators: Dan Parsons, Ben Price

Submitter: Dan Parsons

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