Workflows

What is a Workflow?
31 Workflows visible to you, out of a total of 31
Stable

Detects SNPs and INDELs.

Type: Galaxy

Creators: None

Submitter: Ambarish Kumar

Stable

Author: AMBARISH KUMAR er.ambarish@gmail.com & ambari73_sit@jnu.ac.in

This is a proposed standard operating procedure for genomic variant detection using GATK4.

It is hoped to be effective and useful for getting SARS-CoV-2 genome variants.

It uses Illumina RNASEQ reads and genome sequence.

Type: Common Workflow Language

Creator: Ambarish Kumar

Submitter: Ambarish Kumar

Stable

Author: AMBARISH KUMAR er.ambarish@gmail.com; ambari73_sit@jnu.ac.in

This is a proposed standard operating procedure for genomic variant detection using VARSCAN.

It is hoped to be effective and useful for getting SARS-CoV-2 genome variants.

It uses Illumina RNASEQ reads and genome sequence.

Type: Common Workflow Language

Creator: Ambarish Kumar

Submitter: Ambarish Kumar

Stable

Author: AMBARISH KUMAR er.ambarish@gmail.com & ambari73_sit@jnu.ac.in

This is a proposed standard operating procedure for genomic variant detection using GATK4.

It is hoped to be effective and useful for getting SARS-CoV-2 genome variants.

It uses Illumina RNASEQ reads and genome sequence.

Type: Common Workflow Language

Creator: Ambarish Kumar

Submitter: Ambarish Kumar

Stable

nf-core/vipr is a bioinformatics best-practice analysis pipeline for assembly and intrahost / low-frequency variant calling for viral samples. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible. Pipeline Steps

Step Main program/s

Trimming, combining of read-pairs per sample and QC Skewer, FastQC

Decontamination ...

Type: Nextflow

Creator: Andreas Wilm and October SESSIONS and Paola Florez DE SESSIONS and ZHU Yuan and Shuzhen SIM and CHU Wenhan Collins

Submitter: Laura Rodriguez-Navas

Stable

nfcore/viralrecon is a bioinformatics analysis pipeline used to perform assembly and intrahost/low-frequency variant calling for viral samples. The pipeline currently supports metagenomics and amplicon sequencing data derived from the Illumina sequencing platform. This pipeline is a re-implementation of the SARS_Cov2_consensus-nf and SARS_Cov2_assembly-nf pipelines initially developed by Sarai Varona and Sara Monzon from BU-ISCIII. Porting both of these pipelines to nf-core was an international ...

Type: Nextflow

Creator: Sarai Varona and Miguel Juliá and Sara Monzon and Alexander Peltzer and Alison Meynert and Edgar Garriga Nogales and Erik Garrison and Gisela Gabernet and Harshil Patel and Joao Curado and Jose Espinosa-Carrasco and Katrin Sameith and Marta Pozuelo and Maxime Garcia and Michael Heuer and Phil Ewels and Simon Heumos and Stephen Kelly and Thanh Le Viet and Isabel Cuesta

Submitter: Hervé Ménager

This workflow is used for the virtual screening of the SARS-CoV-2 main protease (de.NBI-cloud, STFC). It includes Charge enumeration, Generation of 3D conformations, Preparation of active site for docking using rDock, Docking, Scoring and Selection of compounds available. More info can be found at https://covid19.galaxyproject.org/cheminformatics/

Type: Galaxy

Creator: Tim Dudgeon, Simon Bray, Gianmauro Cuccuru, Björn Grüning, Rachael Skyner, Jack Scantlebury, Susan Leung, Frank von Delft

Submitter: Bert Droesbeke

This workflow combines SDF files from all fragments into a single dataset and filters to include only the lowest (best) scoring pose for each compound. This file of optimal poses for all ligands is used to compare to a database of Enamine and Chemspace compounds to select the best scoring 500 matches. More info can be found at https://covid19.galaxyproject.org/cheminformatics/

Type: Galaxy

Creator: Tim Dudgeon, Simon Bray, Gianmauro Cuccuru, Björn Grüning, Rachael Skyner, Jack Scantlebury, Susan Leung, Frank von Delft

Submitter: Bert Droesbeke

This workflow generates binding scores that correlate well with binding affinities using an additional tool TransFS, developed at Oxford University. More info can be found at https://covid19.galaxyproject.org/cheminformatics/

Type: Galaxy

Creator: Tim Dudgeon, Simon Bray, Gianmauro Cuccuru, Björn Grüning, Rachael Skyner, Jack Scantlebury, Susan Leung, Frank von Delft

Submitter: Bert Droesbeke

This workflow generates binding scores that correlate well with binding affinities using an additional tool SuCOS Max, developed at Oxford University. More info can be found at https://covid19.galaxyproject.org/cheminformatics/

Type: Galaxy

Creator: Tim Dudgeon, Simon Bray, Gianmauro Cuccuru, Björn Grüning, Rachael Skyner, Jack Scantlebury, Susan Leung, Frank von Delft

Submitter: Bert Droesbeke

Powered by
(v.1.16.0-main)
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH