EmpiricalReads2Map

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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).

Documentation

Check the description of the inputs for the pipelines:

• EmpiricalReads2Map (EmpiricalSNPCalling and EmpiricalMaps)

• SimulatedReads2Map

Check how to evaluate the workflows results in Reads2MapApp Shiny:

• Reads2MapApp

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

• A Guide to Build High-Density Linkage Maps

Check more information and examples of usage in:

• Taniguti, C. H., Taniguti, L. M., Amadeu, R. R., Mollinari, M., Da, G., Pereira, S., Riera-Lizarazu, O., Lau, J., Byrne, D., de Siqueira Gesteira, G., De, T., Oliveira, P., Ferreira, G. C., & Franco Garcia, A. A. Developing best practices for genotyping-by-sequencing analysis using linkage maps as benchmarks. BioRxiv. https://doi.org/10.1101/2022.11.24.517847

Third-party software and images

• BWA in us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.5.7-2021-06-09_16-47-48Z: Used to align simulated reads to reference;
• cutadapt in cristaniguti/ pirs-ddrad-cutadapt:0.0.1: Trim simulated reads;
• ddRADseqTools in cristaniguti/ pirs-ddrad-cutadapt:0.0.1: Set of applications useful to in silico design and testing of double digest RADseq (ddRADseq) experiments;
• Freebayes in Cristaniguti/freebayes:0.0.1: Variant call step;
• GATK in us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.5.7-2021-06-09_16-47-48Z: Variant call step using Haplotype Caller, GenomicsDBImport and GenotypeGVCFs;
• PedigreeSim in cristaniguti/reads2map:0.0.1: Simulates progeny genotypes from parents genotypes for different types of populations;
• picard in us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.5.7-2021-06-09_16-47-48Z: Process alignment files;
• pirs in cristaniguti/ pirs-ddrad-cutadapt:0.0.1: To generate simulates paired-end reads from a reference genome;
• samtools in us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.5.7-2021-06-09_16-47-48Z: Process alignment files;
• SimuSCoP in cristaniguti/simuscopr:0.0.1: Exome and WGS Illumina reads simulations;
• RADinitio in cristaniguti/radinitio:0.0.1: RADseq Illumina reads simulation;
• SuperMASSA in cristaniguti/reads2map:0.0.1: Efficient Exact Maximum a Posteriori Computation for Bayesian SNP Genotyping in Polyploids;
• bcftools in lifebitai/bcftools:1.10.2: utilities for variant calling and manipulating VCFs and BCFs;
• vcftools in cristaniguti/split_markers:0.0.1: program package designed for working with VCF files.
• MCHap in cristaniguti/mchap:0.7.0: Polyploid micro-haplotype assembly using Markov chain Monte Carlo simulation.

R packages

• OneMap in cristaniguti/reads2map:0.0.1: Is a software for constructing genetic maps in experimental crosses: full-sib, RILs, F2 and backcrosses;
• Reads2MapTools in cristaniguti/reads2map:0.0.1: Support package to perform mapping populations simulations and genotyping for OneMap genetic map building
• GUSMap: Genotyping Uncertainty with Sequencing data and linkage MAPping
• updog in cristaniguti/reads2map:0.0.1: Flexible Genotyping of Polyploids using Next Generation Sequencing Data
• polyRAD in cristaniguti/reads2map:0.0.1: Genotype Calling with Uncertainty from Sequencing Data in Polyploids
• Reads2MapApp in cristaniguti/reads2mapApp:0.0.1: Shiny app to evaluate Reads2Map workflows results
• simuscopR in cristaniguti/reads2map:0.0.1: Wrap-up R package for SimusCop simulations.