Workflows

What is a Workflow?
1195 Workflows visible to you, out of a total of 1276
Stable

The workflow takes a (trimmed) Long reads collection, runs Meryl to create a K-mer database, Genomescope2 to estimate genome properties and Smudgeplot to estimate ploidy (optional). The main results are K-mer database and genome profiling plots, tables, and values useful for downstream analysis. Default K-mer length and ploidy for Genomescope are 31 and 2, respectively.

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

DOI: 10.48546/workflowhub.workflow.603.1

Stable

The workflow takes a Long Reads collection, Pri/Alt contigs, and the values for transition parameter and max coverage depth (calculated from WF1) to run Purge_Dups. It produces purged Pri and Alt contigs assemblies, 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.1163.1

Stable

The workflow takes trimmed HiC paired-end reads collection, and Pri/Alt assemblies to produce a scaffolded primary assembly (and alternate contigs) using YaHS. It also runs Pretext and all the QC analyses (gfastats, BUSCO, and Merqury).

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

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: 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

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

Application that perform the multiplication between matrices.

Type: COMPSs

Creator: Raül Sirvent

Submitter: Nicolò Giacomini

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

Type: Nextflow

Creators: Luisa Santus, Jose Espinosa Carrasco

Submitter: WorkflowHub Bot

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

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

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