Workflows

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738 Workflows visible to you, out of a total of 793
ERGA ONT+Illumina Collapsed Purge+QC v2311 (WF3)
Work-in-progress

The workflow takes a trimmed Illumina WGS paired-end reads collection, Collapsed contigs, and the values for transition parameter and max coverage depth (calculated from WF1) to run Purge_Dups. It produces purged Collapsed contigs assemblies, and runs all the QC analysis (gfastats, BUSCO, and Merqury).

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

ERGA Profiling Illumina v2311 (WF1)
Stable

The workflow takes a trimmed Illumina paired-end reads collection, runs Meryl to create a K-mer database, Genomescope2 to estimate genome properties and Smudgeplot to estimate ploidy. The main results are K-mer ddatabase and genome profiling plots, tables, and values useful for downstream analysis. Default K-mer length and ploidy for Genomescope are 21 and 2, respectively.

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

ERGA DataQC ONT v2311 (WF0)
Stable

The workflow takes ONT reads collection, runs SeqKit and Nanoplot. The main outputs are a table and plots of raw reads stats.

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

Phylogeny reconstruction using bacpage

BACPAGE

This repository contains an easy-to-use pipeline for the assembly and analysis of bacterial genomes using ONT long-read or Illumina short-read technology. Read the complete documentation and instructions for bacpage and each of its functions here

Introduction

Advances in sequencing technology during the COVID-19 pandemic has led to massive increases in the generation of sequencing data. Many bioinformatics tools ...

Type: Workflow Description Language

Creators: None

Submitter: Nathaniel Matteson

ERGA HiFi Hap1Hap2 Purge+QC v2309 (WF3)
Stable

The workflow takes a trimmed HiFi reads collection, Hap1/Hap2 contigs, and the values for transition parameter and max coverage depth (calculated from WF1) to run Purge_Dups. It produces purged Hap1 and Hap2 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.606.2

fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex

This workflow processes the CMO fastqs with CITE-seq-Count and include the translation step required for cellPlex processing. In parallel it processes the Gene Expresion fastqs with STARsolo, filter cells with DropletUtils and reformat all outputs to be easily used by the function 'Read10X' from Seurat.

Type: Galaxy

Creators: Lucille Delisle, Mehmet Tekman, Hans-Rudolf Hotz, Daniel Blankenberg, Wendi Bacon

Submitter: WorkflowHub Bot

Reference-based assembly with bacpage
Work-in-progress

bacpage{width=500}

This repository contains an easy-to-use pipeline for the assembly and analysis of bacterial genomes using ONT long-read or Illumina short-read technology.

Introduction

Advances in sequencing technology during the COVID-19 pandemic has led to massive increases in the generation of sequencing data. Many bioinformatics tools have been developed to analyze this data, but very few tools ...

Type: Workflow Description Language

Creators: None

Submitter: Nathaniel Matteson

Somatic-ShortV-nf
Work-in-progress

This is a Nextflow implementaion of the GATK Somatic Short Variant Calling workflow. This workflow can be used to discover somatic short variants (SNVs and indels) from tumour and matched normal BAM files following GATK's Best Practices Workflow. The workflowis currently optimised to run efficiently and at scale on the National Compute Infrastructure, Gadi.

Type: Nextflow

Creators: Nandan Deshpande, Tracy Chew, Cali Willet, Georgina Samaha

Submitter: Georgina Samaha

DOI: 10.48546/workflowhub.workflow.691.1

Lanczos SVD
Stable

Name: Lanczos SVD Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum4

Lanczos SVD for computing singular values needed to reach an epsilon of 1e-3 on a matrix of (150000, 150). The input matrix is generated synthetically. This application used dislib-0.9.0

Type: COMPSs

Creators: Fernando Vázquez-Novoa, Workflows and Distributed Computing

Submitter: Fernando Vázquez-Novoa

DOI: 10.48546/workflowhub.workflow.690.1

mRNA-Seq BY-COVID Pipeline: Analysis
Work-in-progress

Analyse Bulk RNA-Seq data in preparation for downstream Pathways analysis with MINERVA

Type: Galaxy

Creators: Iacopo Cristoferi, Helena Rasche, Clinical Bioinformatics Unit, Pathology Department, Eramus Medical Center

Submitter: Helena Rasche

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