Workflows

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604 Workflows visible to you, out of a total of 648
Fgenesh annotation -TSI

This is part of a series of workflows to annotate a genome, tagged with TSI-annotation. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

The workflows can be run in this order:

  • Repeat masking
  • RNAseq QC and read trimming
  • Find transcripts
  • Combine transcripts
  • Extract transcripts
  • Convert formats
  • Fgenesh annotation

Type: Galaxy

Creator: Luke Silver

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.881.1

Workflow 3: AMR - SeqSero2/SISTR
Work-in-progress

With this galaxy pipeline you can use Salmonella sp. next generation sequencing results to predict bacterial AMR phenotypes and compare the results against gold standard Salmonella sp. phenotypes obtained from food.

This pipeline is based on the work of the National Food Agency of Canada. Doi: 10.3389/fmicb.2020.00549

Type: Galaxy

Creators: None

Submitter: Dennis Dollée

Workflow 1: AbritAMR
No description specified

Type: Galaxy

Creators: None

Submitter: Dennis Dollée

JAX NGS Operations Nextflow DSL2 Pipelines
Stable

DOI

JAX NGS Operations Nextflow DSL2 Pipelines

This repository contains production bioinformatic analysis pipelines for a variety of bulk 'omics data analysis. Please see the Wiki documentation associated with this repository for all documentation and available analysis workflows.

Type: Nextflow

Creators: Michael Lloyd, Brian Sanderson, Barry Guglielmo, Sai Lek, Peter Fields, Harshpreet Chandok, Carolyn Paisie, Gabriel Rech, Ardian Ferraj, Anuj Srivastava

Submitter: Michael Lloyd

DOI: 10.48546/workflowhub.workflow.874.1

Tango: Numerical reconciliation of bacterial fermentation in cheese production
Stable

Complete workflow for TANGO as reported in Lecomte et al (2024), "Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling", Metabolic Eng. 83:24-38 https://doi.org/10.1016/j.ymben.2024.02.014

  1. Parameters for individual models are obtained by optimization
  2. Individual dynamics and community dynamics are simulated
  3. Figures for the manuscript are assembled from the results.

Type: Common Workflow Language

Creators: None

Submitter: David James Sherman

Assembly-Hifi-Trio-phasing-VGP5/main

Assembly with Hifi reads and Trio Data

Generate phased assembly based on PacBio Hifi Reads using parental Illumina data for phasing

Inputs

  1. Hifi long reads [fastq]
  2. Concatenated Illumina reads : Paternal [fastq]
  3. Concatenated Illumina reads : Maternal [fastq]
  4. K-mer database [meryldb]
  5. Paternal hapmer database [meryldb]
  6. Maternal hapmer database [meryldb]
  7. Genome profile summary generated by Genomescope [txt]
  8. Genome model parameters generated by Genomescope [tabular]

...

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

qiime2-I-import/QIIME2-Ia import multiplexed data single end

Importing single-end multiplexed data (not demultiplexed yet)

Type: Galaxy

Creators: Debjyoti Ghosh, Helmholtz-Zentrum für Umweltforschung - UFZ

Submitter: WorkflowHub Bot

qiime2-II-denoising/QIIME2-IIa denoising and feature table creation for single ended data

Use DADA2 for sequence quality control. DADA2 is a pipeline for detecting and correcting (where possible) Illumina amplicon sequence data. As implemented in the q2-dada2 plugin, this quality control process will additionally filter any phiX reads (commonly present in marker gene Illumina sequence data) that are identified in the sequencing data, and will filter chimeric sequences.

Type: Galaxy

Creators: Debjyoti Ghosh, Helmholtz-Zentrum für Umweltforschung - UFZ

Submitter: WorkflowHub Bot

consensus-peaks/consensus-peaks-chip-sr

This workflow takes as input SR BAM from ChIP-seq. It calls peaks on each replicate and intersect them. In parallel, each BAM is subsetted to smallest number of reads. Peaks are called using all subsets combined. Only peaks called using a combination of all subsets which have summits intersecting the intersection of at least x replicates will be kept.

Type: Galaxy

Creator: Lucille Delisle

Submitter: WorkflowHub Bot

polish-with-long-reads/main

Racon polish with long reads, x4

Type: Galaxy

Creator: Anna Syme

Submitter: WorkflowHub Bot

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