Workflows

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558 Workflows visible to you, out of a total of 602

var-PE

CWL workflow SARS-CoV-2

Stable

Analysis of variation within individual COVID-19 samples using bowtie2, bwa, fastp, multiqc , picard ,samtools, snpEff Workflow, tools and data are available on https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2/tree/master/Variation This worklow was ported into CWL from a Galaxy Workflow ( https://github.com/galaxyproject/SARS-CoV-2/tree/master/genomics/4-Variation migrated to CWL).

Type: Common Workflow Language

Creator: Camille Juigné

Submitter: Camille Juigné

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Created: 8th Jun 2020 at 15:57, Last updated: 30th Jun 2020 at 08:58

Views: 2353, Downloads: 376

Genomic variants - SNPs and INDELs detection using SAMTools.

CWL workflow SARS-CoV-2

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 SAMTools.

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

Creators: None

Submitter: Ambarish Kumar

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Created: 17th Jun 2020 at 08:41, Last updated: 27th Jun 2020 at 02:27

Views: 2751, Downloads: 400

COVID-19: VARSCAN

GalaxyProject SARS-CoV-2

Stable

Detects SNPs and INDELs using VARSCAN2.

Type: Galaxy

Creators: None

Submitter: Ambarish Kumar

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Created: 18th Jun 2020 at 23:57

Views: 3237, Downloads: 191

COVID-19: GATK4

GalaxyProject SARS-CoV-2

Stable

Detects SNPs and INDELs.

Type: Galaxy

Creators: None

Submitter: Ambarish Kumar

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Created: 18th Jun 2020 at 16:49

Views: 2866, Downloads: 174

Genomic variants - SNPs and INDELs detection using GATK4 spark based tools.

CWL workflow SARS-CoV-2

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

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Created: 17th Jun 2020 at 07:38

Views: 2268, Downloads: 189

Genomic variants - SNPs and INDELs detection using VARSCAN2.

CWL workflow SARS-CoV-2

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

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Created: 17th Jun 2020 at 07:24

Views: 2177, Downloads: 207

Genomic variants - SNPs and INDELs detection using GATK4.

CWL workflow SARS-CoV-2

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

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Created: 17th Jun 2020 at 07:11

Views: 2219, Downloads: 189

nf-core/vipr

nf-core viralrecon

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

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Created: 14th May 2020 at 15:42, Last updated: 2nd Jun 2020 at 11:49

Views: 3910, Downloads: 366

nf-core/viralrecon

nf-core viralrecon

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

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Created: 14th May 2020 at 15:10, Last updated: 2nd Jun 2020 at 11:46

Views: 3374, Downloads: 374

Pathway Ranker

IBISBA Workflows

Stable

The workflow runs the RetroSynthesis algorithm to generate a collection of heterologous pathways in a host organism of choice, converts them to SBML files, performs analysis on the pathways to then rank the theoretical best performing ones.

Type: Galaxy

Creator: Melchior du Lac

Submitter: Melchior du Lac

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Created: 29th May 2020 at 12:19

Views: 3025, Downloads: 157

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