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82 Workflows visible to you, out of a total of 101

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

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Type: Galaxy

Creator: Wolfgang Maier

Submitter: Simone Leo

Stable

This implementation was done for the ELIXIR EXCELERATE Demonstrator to be run on WES-TES environment.

There is also task related to input file transfer (curl) and the output file transfer to a private FTP server. The needed URLs and FTP credential are given as input parameters.

The input files are assumed to come from a web server. Idea there is to make some configurations more modular and some tools like lftp or curl have easier to write script parameter files instead of command line parameters.

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Type: Common Workflow Language

Creators: Laura Rodriguez-Navas, José Mª Fernández

Submitter: Laura Rodriguez-Navas

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

...

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

Stable
No description specified

Type: Nextflow

Creators: José Mª Fernández, Víctor Fernández

Submitters: Laura Rodriguez-Navas, José Mª Fernández

Stable
No description specified

Type: Common Workflow Language

Creator: 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

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