Workflows

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844 Workflows visible to you, out of a total of 923
gromacs-dctmd/main

Perform dcTMD free energy simulations and calculations

Type: Galaxy

Creators: Simon Bray, Simon Bray

Submitter: WorkflowHub Bot

CWL4IncorporateTSSintoGXF (paired-end file)

License GitHub last commit (branch) run with docker Lab Website

 

CWL4IncorporateTSSintoGXF

This ...

Type: Common Workflow Language

Creators: Ryo Nozu, Sora Yonezawa

Submitter: Sora Yonezawa

NGS Equimolar Pooling Calculator
Stable

NGS Equimolar Pooling Calculator

A web-based tool for calculating equimolar pooling volumes from complex sub-pools for Next-Generation Sequencing (NGS).

About

This calculator helps researchers determine the correct volumes to take from each pool when combining multiple complex sub-pools of NGS libraries for sequencing. It ensures that each individual sample contributes an equal number of molecules to the final sequencing run, resulting in more balanced coverage.

Features

  • Calculate ...

Type: Unrecognized workflow type

Creator: Ben Price

Submitter: Ben Price

DOI: 10.48546/workflowhub.workflow.1344.1

Gene Fetch
Work-in-progress

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

Gene Fetch

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

nf-core/hlatyping

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

Type: Nextflow

Creators: Christopher Mohr, Alexander Peltzer, Sven Fillinger

Submitter: WorkflowHub Bot

gSpreadComp

gSpreadComp: Streamlining Microbial Community Analysis for Resistance, Virulence, and Plasmid-Mediated Spread

Overview

gSpreadComp is a UNIX-based, modular bioinformatics toolkit designed to streamline comparative genomics for analyzing microbial communities. It integrates genome annotation, gene spread calculation, plasmid-mediated horizontal gene transfer (HGT) detection and resistance-virulence ranking within the analysed microbial community to help researchers identify potential ...

Type: Shell Script

Creator: Jonas Kasmanas

Submitter: Jonas Kasmanas

DOI: 10.48546/workflowhub.workflow.1340.3

COMPSs Matrix Multiplication resourceUsage profiling example MN5 MSIZE=20 BSIZE=768 7 Nodes total
Stable

COMPSs Matrix Multiplication resourceUsage profiling example.

MN5 MSIZE=20 BSIZE=768 7 Nodes (6 workers) (--num_nodes=7 --worker_in_master_cpus=0).

  • Total number of tasks: 20^3 = 8000
  • Maximum code parallelism: 20^2 = 400
  • Total cores: 112*6 = 672
  • Maximum utilisation: 400 / 112 = 3,57 Nodes

Overall stats from "pycompss inspect":

│ └── overall 
│ ├── matmul_tasks 
│ │ └── multiply 
│ │ ├── maxTime = 91,111 ms 
│ │ ├── executions = 8,000 
│ │ ├── avgTime = 84,839 ms 
│ │ └── minTime = 79,278 ms
...

Type: COMPSs

Creators: Raül Sirvent, Rosa M Badia

Submitter: Raül Sirvent

Matrix Multiplication – resource usage visualization

Application that perform the multiplication between matrices. In this experiment, a new profiling visualization is available, showing the resource usage such as CPU, memory, data read and written to disk, and data sent and received over the network.

Type: COMPSs

Creators: Raül Sirvent, Nicolò Giacomini

Submitter: Nicolò Giacomini

tissue-microarray-analysis/main

Complete multiplex tissue image (MTI) analysis pipeline for tissue microarray (TMA) data imaged using cyclic immunofluorescence: Performs illumination correction, stitching and registration, and tissue microarray segmentation. Tissue-segmented images undergo nuclear segmentation, cell/nuclei feature quantification (mean marker intensities, cell coordinates, and morphological features), and cell phenotyping. Produces outputs that are compatible with downstream single-cell/spatial analysis and ...

Type: Galaxy

Creator: Cameron Watson

Submitter: WorkflowHub Bot

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