marcguery/malaria-barcodes-genomes-gambia

# Scripts, data and figures of Guery *et al.* 2024 This repository contains the pipeline, data and figures included in: Guery, M.-A., Ceesay, S., Drammeh, S., Jaiteh, F. K., d’Alessandro, U., Bousema, T., Conway, D. J., & Claessens, A. (2024). Household clustering and seasonal genetic variation of Plasmodium falciparum at the community-level in The Gambia. *eLife*, *13*. doi.org. # Pipeline The details of this pipeline are described in the methods section of the corresponding article. The script `barcode-genome_pipeline.R` is the main script controlling each step of the pipeline. Beware that some steps require the output of previous ones. The script `make-tables.R` uses the output of the pipeline to produce the tables attached with the article. ## Environment The pipeline was run with R version 4.3.3 on Ubuntu 22. ```R ─ Session info ──────────────────────────────────────────────────────────────────────────────────────── setting value version R version 4.3.3 (2024-02-29) os Ubuntu 22.04.5 LTS system x86_64, linux-gnu ui RStudio language (EN) collate C.UTF-8 ctype C.UTF-8 tz Europe/Paris date 2025-01-21 rstudio 2024.12.0+467 Kousa Dogwood (desktop) pandoc 2.9.2.1 @ /usr/bin/pandoc ─ Packages ──────────────────────────────────────────────────────────────────────────────────────────── package * version date (UTC) lib source ape * 5.7-1 2023-03-13 [1] CRAN (R 4.3.2) binom * 1.1-1.1 2022-05-02 [1] CRAN (R 4.3.3) BiocGenerics * 0.48.1 2023-11-01 [1] Bioconductor cli 3.6.3 2024-06-21 [1] CRAN (R 4.3.3) colorspace 2.1-1 2024-07-26 [1] CRAN (R 4.3.3) cowplot * 1.1.3 2024-01-22 [1] CRAN (R 4.3.2) digest 0.6.36 2024-06-23 [1] CRAN (R 4.3.3) dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.3.2) fansi 1.0.6 2023-12-08 [1] CRAN (R 4.3.2) farver 2.1.2 2024-05-13 [1] CRAN (R 4.3.3) generics 0 …