Workflows

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124 Workflows visible to you, out of a total of 184
Stable

COnSensus Interaction Network InFErence Service

Inference framework for reconstructing networks using a consensus approach between multiple methods and data sources.

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Reference

[Manica, Matteo, Charlotte, Bunne, Roland, Mathis, Joris, Cadow, Mehmet Eren, Ahsen, Gustavo A, Stolovitzky, and María Rodríguez, Martínez. "COSIFER: a python package for the consensus inference of molecular ...

Stable

COnSensus Interaction Network InFErence Service

Inference framework for reconstructing networks using a consensus approach between multiple methods and data sources.

alt text

Reference

[Manica, Matteo, Charlotte, Bunne, Roland, Mathis, Joris, Cadow, Mehmet Eren, Ahsen, Gustavo A, Stolovitzky, and María Rodríguez, Martínez. "COSIFER: a python package for the consensus inference of molecular ...

Type: Common Workflow Language

Creators: José Mª Fernández, Laura Rodriguez-Navas

Submitter: Laura Rodriguez-Navas

COVID-19: variation analysis on ARTIC ONT data

This workflow for ONT-sequenced ARTIC data is modeled after the alignment/variant-calling steps of the ARTIC pipeline. It performs, essentially, the same steps as that pipeline’s minion command, i.e. read mapping with minimap2 and variant calling with medaka. Like the Illumina ARTIC workflow it uses ivar for primer trimming. Since ONT-sequenced reads have a much ...

Type: Galaxy

Creator: Wolfgang Maier

Submitter: WorkflowHub Sandbox Bot

COVID-19: variation analysis on WGS PE data

This workflows performs single end read mapping with bowtie2 followed by sensitive variant calling across a wide range of AFs with lofreq and variant annotation with snpEff 4.5covid19.

Type: Galaxy

Creator: Wolfgang Maier

Submitter: WorkflowHub Sandbox Bot

COVID-19: variation analysis on WGS PE data

This workflows performs paired end read mapping with bwa-mem followed by sensitive variant calling across a wide range of AFs with lofreq and variant annotation with snpEff 4.5covid19.

Type: Galaxy

Creator: Wolfgang Maier

Submitter: WorkflowHub Sandbox Bot

COVID-19: variation analysis on ARTIC PE data

The workflow for Illumina-sequenced ARTIC data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but adds extra logic for trimming ARTIC primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by ARTIC primer-binding site mutations and excludes reads derived from such "tainted" amplicons ...

Type: Galaxy

Creator: Wolfgang Maier

Submitter: WorkflowHub Sandbox Bot

Stable
  1. Name of the application: Adapter removal hello world
  2. Name of the application: Mapping and bam sorting goodbye world

1. Name of the application: Adapter removal hello world 2. Name of the application: Mapping and bam sorting goodbye world

Type: Taverna

Creators: None

Submitter: Finn Bacall

DOI: 10.81082/dev-workflowhub.workflow.136.1

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