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] "2023-03-24 17:36:36 UTC"
##    user  system elapsed 
##   0.553   0.104   0.585
## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
##  setting  value
##  version  R Under development (unstable) (2023-03-16 r83996)
##  os       Ubuntu 22.04.2 LTS
##  system   x86_64, linux-gnu
##  ui       X11
##  language (EN)
##  collate  en_US.UTF-8
##  ctype    en_US.UTF-8
##  tz       UTC
##  date     2023-03-24
##  pandoc   2.19.2 @ /usr/local/bin/ (via rmarkdown)
## 
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
##  package     * version date (UTC) lib source
##  bookdown      0.33    2023-03-06 [1] CRAN (R 4.3.0)
##  bslib         0.4.2   2022-12-16 [2] CRAN (R 4.3.0)
##  cachem        1.0.7   2023-02-24 [2] CRAN (R 4.3.0)
##  cli           3.6.0   2023-01-09 [2] CRAN (R 4.3.0)
##  digest        0.6.31  2022-12-11 [2] CRAN (R 4.3.0)
##  evaluate      0.20    2023-01-17 [2] CRAN (R 4.3.0)
##  fastmap       1.1.1   2023-02-24 [2] CRAN (R 4.3.0)
##  htmltools     0.5.4   2022-12-07 [2] CRAN (R 4.3.0)
##  jquerylib     0.1.4   2021-04-26 [2] CRAN (R 4.3.0)
##  jsonlite      1.8.4   2022-12-06 [2] CRAN (R 4.3.0)
##  knitr         1.42    2023-01-25 [2] CRAN (R 4.3.0)
##  R6            2.5.1   2021-08-19 [2] CRAN (R 4.3.0)
##  rlang         1.1.0   2023-03-14 [2] CRAN (R 4.3.0)
##  rmarkdown     2.20    2023-01-19 [2] CRAN (R 4.3.0)
##  rstudioapi    0.14    2022-08-22 [2] CRAN (R 4.3.0)
##  sass          0.4.5   2023-01-24 [2] CRAN (R 4.3.0)
##  sessioninfo * 1.2.2   2021-12-06 [2] CRAN (R 4.3.0)
##  xfun          0.37    2023-01-31 [2] CRAN (R 4.3.0)
##  yaml          2.3.7   2023-01-23 [2] CRAN (R 4.3.0)
## 
##  [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 2023-03-24 17:36:36.103311.