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Workflow Type: Workflow Description Language

Development Reads2Map


Reads2Map presents a collection of WDL workflows to build linkage maps from sequencing reads. Each workflow release is described in the Read2Map releases page.

The main workflows are the EmpiricalReads2Map.wdl and the SimulatedReads2Map.wdl. The EmpiricalReads2Map.wdl is composed by the EmpiricalSNPCalling.wdl that performs the SNP calling, and the EmpiricalMaps.wdl that performs the genotype calling and map building in empirical reads. The SimulatedReads2Map.wdl simulates Illumina reads for RADseq, exome, or WGS data and performs the SNP and genotype calling and genetic map building.

By now, GATK, Freebayes are included for SNP calling; updog, polyRAD, SuperMASSA for dosage calling; and OneMap, and GUSMap for linkage map build.


How to use

Multiple systems are available to run WDL workflows such as Cromwell, miniWDL, and dxWDL. See further information in the openwdl documentation.

To run a pipeline, first navigate to Reads2Map releases page, search for the pipeline tag you which to run, and download the pipeline’s assets (the WDL workflow, the JSON, and the ZIP with accompanying dependencies).


Check the description of the inputs for the pipelines:

Check how to evaluate the workflows results in Reads2MapApp Shiny:

Once you selected the best pipeline using a subset of your data, you can build a complete high-density linkage map:

Check more information and examples of usage in:

Third-party software and images

R packages

Version History

main @ 09cc213 (earliest) Created 29th Nov 2022 at 20:09 by Cristiane Taniguti

Merge pull request #56 from Cristianetaniguti/joint_EmpiricalReads

Joint empirical reads

Frozen main 09cc213
help Creators and Submitter
Taniguti, C. (2022). EmpiricalReads2Map. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.409.1

Views: 1346   Downloads: 112

Created: 29th Nov 2022 at 20:09

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