README.md

In bahlolab/HaplotypReportR: Generate Reports using HaplotypR

HaplotypReportR

Purpose

HaplotypReportR is an R package for generating HTML reports for AmpSeq experiments using the R pacakage HaplotypR.

Pipeline overview

1) Split input FASTQ files into pieces for parallel processing 2) Demultiplex samples using HaplotypR::demultiplexReads 3) Demultiplex sample-markers using HaplotypR::demultiplexByMarker 5) Gather sample-marker FASTQ files and optionally subsample high read counts 4) Fuse sample-marker paired reads using HaplotypR::bindAmpliconReads or HaplotypR::mergeAmpliconReads 5) Call SNPs in samples with HaplotypR::calculateMismatchFrequencies and HaplotypR::callGenotype 6) Call sample haplotypes with HaplotypR::createFinalHaplotypTable 7) Save results and generate HTML report including various summary data visualisations

Enhancements

1) Parallel processing using the future and furrr packages 2) Read quality profile plotting 3) A named panel of known haplotypes for each marker may be included, allowing easier comparison of haplotypes identified over multiple experiments 4) Visualisation of Majority Haplotypes detected in each sample

Installation

1) First follow HaplotypR installation instructions at https://github.com/lerch-a/HaplotypR 2) Make sure all required packages are installed. This can be done by running the following code: ```R installed_packages <- rownames(installed.packages())

cran_required <- c("cowplot", "devtools", "dplyr", "htmltools", "forcats", "furrr", "future", "ggplot2", "ggfittext", "openssl", "purrr", "readr", "rlang", "rmarkdown", "stringr", "tidyr", "tools", "BiocManager") cran_install <- setdiff(cran_required, installed_packages)

if (length(cran_install) > 0) { install.packages(cran_install) }

bioc_required <- c("DECIPHER", "ShortRead", "Biostrings") bioc_install <- setdiff(bioc_required, installed_packages)

if (length(bioc_install) > 0) { BiocManager::install(bioc_install) } 3) Install HaplotypReportR from github:R devtools::install_github("bahlolab/HaplotypReportR") ```

Usage

• The following example uses the example dataset included with HaplotypR ```R library(HaplotypReportR)

example_data <- get_haplotypr_example_data()

report_haplotypes(run_name = 'Example', sample_table = example_data$sample_table, marker_table = example_data$marker_table, barcodes_fwd = example_data$barcodes_fwd, barcodes_rev = example_data$barcodes_rev, reads_fwd = example_data$reads_fwd, reads_rev = example_data$reads_rev, out_dir = 'example_report', read_join_strategy = 'bind') `` * **Note**: it is recommended to leaveread_join_strategyset to the default value of'auto', however'bind'works better in this example * For complete documentation seehelp(report_haplotypes)`

Citations

HaplotypR

The HaplotypR project was developed by Anita Lerch. A paper with more details about the program is available from:

• Lerch, A. et al. Development Of Amplicon Deep Sequencing Markers And Data Analysis Pipeline For Genotyping Multi-Clonal Malaria Infections. BMC Genomics (2017), 18(1), p.864, http://dx.doi.org/10.1186/s12864-017-4260-y.
• Lerch, A. et al. Longitudinal tracking and quantification of individual Plasmodium falciparum clones in complex infections. Sci. Rep. 9, 3333 (2019), http://dx.doi.org/10.1038/s41598-019-39656-7.

bahlolab/HaplotypReportR documentation built on Dec. 2, 2019, 7:36 p.m.