Workflows

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817 Workflows visible to you, out of a total of 891
HP2NET - Framework for Construction of Phylogenetic Networks on High Performance Computing (HPC) Environment

Framework for construction of phylogenetic networks on High Performance Computing (HPC) environment

Introduction

Phylogeny refers to the evolutionary history and relationship between biological lineages related by common descent. Reticulate evolution refers to the origination of lineages through the complete or partial merging of ancestor lineages. Networks may be used to represent lineage independence events in non-treelike phylogenetic processes.

The methodology for reconstructing networks ...

Type: Python

Creators: Rafael Terra, Diego Carvalho

Submitter: Rafael Terra

DOI: 10.48546/workflowhub.workflow.703.1

Pangenome databases provide superior host removal and mycobacteria classification from clinical metagenomic data

Pangenome databases provide superior host removal and mycobacteria classification from clinical metagenomic data

Hall, M, Coin, L., Pangenome databases provide superior host removal and mycobacteria classification from clinical metagenomic data. bioRxiv 2023. doi: [10.1101/2023.09.18.558339][doi]

Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and classification of M. tuberculosis reads.

This repository contains the code and ...

Type: Snakemake

Creator: Michael Hall

Submitter: Michael Hall

DOI: 10.48546/workflowhub.workflow.700.2

ERGA HiC Collapsed Scaffolding+QC YaHS v2311 (WF4)
Work-in-progress

The workflow takes trimmed HiC forward and reverse reads, and one assembly (e.g.: Hap1 or Pri or Collapsed) to produce a scaffolded assembly using YaHS. It also runs all the QC analyses (gfastats, BUSCO, and Merqury).

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

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

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