In brendanf/spoar: SIMD Partial Order Alignment in R

knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.path = "man/figures/README-",
    out.width = "100%"
)

spoar

SPOA is a C++ library for fast alignment and consensus generation of closely related sequences, especially used for long, error-containing reads from third generation sequencers. It allows local, global, and semi-global (overlap) alignment, using linear, affine, or convex gap penalties, and can also weight by quality scores. SPOAR is an R wrapper for SPOA.

Installation instructions

Get the latest stable R release from CRAN. Then install spoar using from Bioconductor the following code:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("spoar")

And the development version from GitHub with:

BiocManager::install("brendanf/spoar")

Example

Here is the first basic example from the SPOR README:

library("spoar")

sequences <- c(
    "CATAAAAGAACGTAGGTCGCCCGTCCGTAACCTGTCGGATCACCGGAAAGGACCCGTAAAGTGATAATGAT",
    "ATAAAGGCAGTCGCTCTGTAAGCTGTCGATTCACCGGAAAGATGGCGTTACCACGTAAAGTGATAATGATTAT",
    "ATCAAAGAACGTGTAGCCTGTCCGTAATCTAGCGCATTTCACACGAGACCCGCGTAATGGG",
    "CGTAAATAGGTAATGATTATCATTACATATCACAACTAGGGCCGTATTAATCATGATATCATCA",
    "GTCGCTAGAGGCATCGTGAGTCGCTTCCGTACCGCAAGGATGACGAGTCACTTAAAGTGATAAT",
    "CCGTAACCTTCATCGGATCACCGGAAAGGACCCGTAAATAGACCTGATTATCATCTACAT"
)

spoaAlign(sequences)

spoaConsensus(sequences)

Citation

Below is the citation output from using citation('spoar') in R. Please run this yourself to check for any updates on how to cite spoar.

print(citation("spoar"), bibtex = TRUE)

Please note that the spoar was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.

Code of Conduct

Please note that the spoar project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Development tools

• Continuous code testing is possible thanks to GitHub actions through r BiocStyle::CRANpkg('usethis'), r BiocStyle::CRANpkg('remotes'), and r BiocStyle::CRANpkg('rcmdcheck') customized to use Bioconductor's docker containers and r BiocStyle::Biocpkg('BiocCheck').
• Code coverage assessment is possible thanks to codecov and r BiocStyle::CRANpkg('covr').
• The documentation website is automatically updated thanks to r BiocStyle::CRANpkg('pkgdown').
• The code is styled automatically thanks to r BiocStyle::CRANpkg('styler').
• The documentation is formatted thanks to r BiocStyle::CRANpkg('devtools') and r BiocStyle::CRANpkg('roxygen2').

For more details, check the dev directory.

This package was developed using r BiocStyle::Biocpkg('biocthis').

brendanf/spoar documentation built on Dec. 19, 2021, 11:43 a.m.