BiocMAP
Lieber Institute for Brain Development, Johns Hopkins Medical CampusLieber Institute for Brain Development, Johns Hopkins Medical CampusCenter for Computational Biology, Johns Hopkins University
lcolladotor@gmail.com
Overview
BiocMAP is a pair of Nextflow-based pipelines for processing raw whole genome bisulfite sequencing data into Bioconductor-friendly bsseq objects in R.
The first BiocMAP module performs speedy alignment to a reference genome by Arioc, and requires GPU resources. Methylation extraction and remaining steps are performed in the second module, optionally on a different computing system where GPUs need not be available.
Diagram representing the “conceptual” workflow traversed by BiocMAP. Here some nextflow processes
are grouped together for simplicity; the exact processes traversed are enumerated here. The red box indicates the FASTQ files are inputs to the pipeline; green coloring denotes major output files from the pipeline; the remaining boxes represent computational steps. Yellow-colored steps are optional or not always performed; for example, lambda pseudoalignment is an optional step intended for experiments with spike-ins of the lambda bacteriophage. Finally, blue-colored steps are ordinary processes which occur on every pipeline execution.
Cite BiocMAP
We hope BiocMAP
will be a useful tool for your research. Please use the following bibtex information to cite this software. Thank you!
@article {Eagles2022.04.20.488947,
author = {Eagles, Nicholas J and Wilton, Richard and Jaffe, Andrew E. and Collado-Torres, Leonardo},
title = {BiocMAP: A Bioconductor-friendly, GPU-Accelerated Pipeline for Bisulfite-Sequencing Data},
year = {2022},
doi = {10.1101/2022.04.20.488947},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://doi.org/10.1101/2022.04.20.488947},
journal = {bioRxiv}
}
This is a project by the R/Bioconductor-powered Team Data Science at the Lieber Institute for Brain Development.
R session information
Details on the R version used for making this book. The source code is available at LieberInstitute/BiocMAP
.
## Load the package at the top of your script
library("sessioninfo")
## Reproducibility information
print('Reproducibility information:')
Sys.time()
proc.time()
options(width = 120)
session_info()
## [1] "Reproducibility information:"
## [1] "2023-09-15 16:55:16 UTC"
## user system elapsed
## 0.557 0.105 0.539
## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
## setting value
## version R version 4.3.1 (2023-06-16)
## os Ubuntu 22.04.3 LTS
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz UTC
## date 2023-09-15
## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
## package * version date (UTC) lib source
## bookdown 0.35 2023-08-09 [1] CRAN (R 4.3.1)
## bslib 0.5.1 2023-08-11 [2] CRAN (R 4.3.1)
## cachem 1.0.8 2023-05-01 [2] CRAN (R 4.3.1)
## cli 3.6.1 2023-03-23 [2] CRAN (R 4.3.1)
## digest 0.6.33 2023-07-07 [2] CRAN (R 4.3.1)
## evaluate 0.21 2023-05-05 [2] CRAN (R 4.3.1)
## fastmap 1.1.1 2023-02-24 [2] CRAN (R 4.3.1)
## htmltools 0.5.6 2023-08-10 [2] CRAN (R 4.3.1)
## jquerylib 0.1.4 2021-04-26 [2] CRAN (R 4.3.1)
## jsonlite 1.8.7 2023-06-29 [2] CRAN (R 4.3.1)
## knitr 1.43 2023-05-25 [2] CRAN (R 4.3.1)
## R6 2.5.1 2021-08-19 [2] CRAN (R 4.3.1)
## rlang 1.1.1 2023-04-28 [2] CRAN (R 4.3.1)
## rmarkdown 2.24 2023-08-14 [2] CRAN (R 4.3.1)
## rstudioapi 0.15.0 2023-07-07 [2] CRAN (R 4.3.1)
## sass 0.4.7 2023-07-15 [2] CRAN (R 4.3.1)
## sessioninfo * 1.2.2 2021-12-06 [2] CRAN (R 4.3.1)
## xfun 0.40 2023-08-09 [2] CRAN (R 4.3.1)
## yaml 2.3.7 2023-01-23 [2] CRAN (R 4.3.1)
##
## [1] /usr/local/lib/R/host-site-library
## [2] /usr/local/lib/R/site-library
## [3] /usr/local/lib/R/library
##
## ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
This book was last updated on 2023-09-15 16:55:16.565399.