[](https://img.shields.io/badge/development-active-blue.svg) [](https://app.circleci.com/pipelines/github/Cristianetaniguti/Reads2Map) ## Reads2Map Reads2Map presents a collection of [WDL workflows](https://openwdl.org/) to build linkage maps from sequencing reads. Each workflow release is described in the [Read2Map releases page](https://github.com/Cristianetaniguti/Reads2Map/releases). 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](https://github.com/broadinstitute/gatk), [Freebayes](https://github.com/ekg/freebayes) are included for SNP calling; [updog](https://github.com/dcgerard/updog), [polyRAD](https://github.com/lvclark/polyRAD), [SuperMASSA](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030906) for dosage calling; and [OneMap](https://github.com/augusto-garcia/onemap), and [GUSMap](https://github.com/tpbilton/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](https://github.com/openwdl/wdl#execution-engines). To run a pipeline, first navigate to [Reads2Map releases page](https://github.com/Cristianetaniguti/Reads2Map/releases), 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)](https://cristianetaniguti.github.io/Tutorials/Reads2Map/EmpiricalReads.html) * [SimulatedReads2Map](https://cristianetaniguti.github.io/Tutorials/Reads2Map/simulatedreads.html) Check how to evaluate the workflows results in Reads2MapApp Shiny: * [Reads2MapApp](https://github.com/Cristianetaniguti/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](https://cristianetaniguti.github.io/Tutorials/onemap/Quick_HighDens/High_density_maps.html) 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](https://www.biorxiv.org/content/10.1101/2022.11.24.517847v2) ## Third-party software and images - [BWA](https://github.com/lh3/bwa) in [us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.5.7-2021-06-09_16-47-48Z](https://console.cloud.google.com/gcr/images/broad-gotc-prod/US/genomes-in-the-cloud): Used to align simulated reads to reference; - [cutadapt](https://github.com/marcelm/cutadapt) in [cristaniguti/ pirs-ddrad-cutadapt:0.0.1](https://hub.docker.com/repository/docker/cristaniguti/pirs-ddrad-cutadapt): Trim simulated reads; - [ddRADseqTools](https://github.com/GGFHF/ddRADseqTools) in [cristaniguti/ pirs-ddrad-cutadapt:0.0.1](https://hub.docker.com/repository/docker/cristaniguti/pirs-ddrad-cutadapt): Set of applications useful to in silico design and testing of double digest RADseq (ddRADseq) experiments; - [Freebayes](https://github.com/ekg/freebayes) in [Cristaniguti/freebayes:0.0.1](): Variant call step; - [GATK](https://github.com/broadinstitute/gatk) in [us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.5.7-2021-06-09_16-47-48Z](https://console.cloud.google.com/gcr/images/broad-gotc-prod/US/genomes-in-the-cloud): Variant call step using Haplotype Caller, GenomicsDBImport and GenotypeGVCFs; - [PedigreeSim](https://github.com/PBR/pedigreeSim?files=1) in [cristaniguti/reads2map:0.0.1](https://hub.docker.com/repository/docker/cristaniguti/reads2map): Simulates progeny genotypes from parents genotypes for different types of populations; - [picard](https://github.com/broadinstitute/picard) in [us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.5.7-2021-06-09_16-47-48Z](https://console.cloud.google.com/gcr/images/broad-gotc-prod/US/genomes-in-the-cloud): Process alignment files; - [pirs](https://github.com/galaxy001/pirs) in [cristaniguti/ pirs-ddrad-cutadapt:0.0.1](https://hub.docker.com/repository/docker/cristaniguti/pirs-ddrad-cutadapt): To generate simulates paired-end reads from a reference genome; - [samtools](https://github.com/samtools/samtools) in [us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.5.7-2021-06-09_16-47-48Z](https://console.cloud.google.com/gcr/images/broad-gotc-prod/US/genomes-in-the-cloud): Process alignment files; - [SimuSCoP](https://github.com/qasimyu/simuscop) in [cristaniguti/simuscopr:0.0.1](https://hub.docker.com/repository/docker/cristaniguti/simuscopr): Exome and WGS Illumina reads simulations; - [RADinitio](http://catchenlab.life.illinois.edu/radinitio/) in [ cristaniguti/radinitio:0.0.1](https://hub.docker.com/repository/docker/cristaniguti/radinitio): RADseq Illumina reads simulation; - [SuperMASSA](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030906) in [cristaniguti/reads2map:0.0.1](https://hub.docker.com/repository/docker/cristaniguti/reads2map): Efficient Exact Maximum a Posteriori Computation for Bayesian SNP Genotyping in Polyploids; - [bcftools](https://github.com/samtools/bcftools) in [lifebitai/bcftools:1.10.2](https://hub.docker.com/r/lifebitai/bcftools): utilities for variant calling and manipulating VCFs and BCFs; - [vcftools](http://vcftools.sourceforge.net/) in [cristaniguti/split_markers:0.0.1](https://hub.docker.com/repository/docker/cristaniguti/split_markers): program package designed for working with VCF files. - [MCHap](https://github.com/PlantandFoodResearch/MCHap) in [cristaniguti/mchap:0.7.0](https://hub.docker.com/repository/docker/cristaniguti/mchap): Polyploid micro-haplotype assembly using Markov chain Monte Carlo simulation. ### R packages - [OneMap](https://github.com/augusto-garcia/onemap) in [cristaniguti/reads2map:0.0.1](https://hub.docker.com/repository/docker/cristaniguti/reads2map): Is a software for constructing genetic maps in experimental crosses: full-sib, RILs, F2 and backcrosses; - [Reads2MapTools](https://github.com/Cristianetaniguti/Reads2MapTools) in [cristaniguti/reads2map:0.0.1](https://hub.docker.com/repository/docker/cristaniguti/reads2map): Support package to perform mapping populations simulations and genotyping for OneMap genetic map building - [GUSMap](https://github.com/tpbilton/GUSMap): Genotyping Uncertainty with Sequencing data and linkage MAPping - [updog](https://github.com/dcgerard/updog) in [cristaniguti/reads2map:0.0.1](https://hub.docker.com/repository/docker/cristaniguti/reads2map): Flexible Genotyping of Polyploids using Next Generation Sequencing Data - [polyRAD](https://github.com/lvclark/polyRAD) in [cristaniguti/reads2map:0.0.1](https://hub.docker.com/repository/docker/cristaniguti/reads2map): Genotype Calling with Uncertainty from Sequencing Data in Polyploids - [Reads2MapApp](https://github.com/Cristianetaniguti/Reads2MapApp) in [cristaniguti/reads2mapApp:0.0.1](https://hub.docker.com/repository/docker/cristaniguti/reads2map): Shiny app to evaluate Reads2Map workflows results - [simuscopR](https://github.com/Cristianetaniguti/simuscopR) in [cristaniguti/reads2map:0.0.1](https://hub.docker.com/repository/docker/cristaniguti/reads2map): Wrap-up R package for SimusCop simulations.