BSgenomeForge is an R/Bioconductor package that provides a set of tools to forge BSgenome data packages. These new tools supersede the old seed-based tools from the BSgenome software package.

About BSgenome data packages

BSgenome data packages are one of the many types of annotation packages available in Bioconductor. They contain the genomic sequences, which comprise chromosome sequences and other DNA sequences, of a particular genome assembly for a given organism. For example BSgenome.Hsapiens.UCSC.hg19 is a BSgenome data package that contains the genomic sequences of the hg19 genome from UCSC. Users can easily and efficiently access the sequences, or portions of the sequences, stored in these packages, via a common API implemented in the BSgenome software package.

Bioconductor currently provides more than 100 BSgenome data packages, for more than 30 organisms. Most of them contain the genomic sequences of UCSC genomes (i.e. genomes supported by the UCSC Genome Browser) or NCBI assemblies. The packages are used in various Bioconductor workflows, as well as in man page examples and vignettes of other Bioconductor packages, typically in conjunction with tools available in the BSgenome and Biostrings software packages. New BSgenome data packages get added on a regular basis, based on user demand.

Useful links

• BSgenome.Hsapiens.UCSC.hg19 landing page: https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19

• List of BSgenome data packages available in Bioconductor: https://bioconductor.org/packages/release/BiocViews.html#___BSgenome

• BSgenome software package landing page (with link to the old “How to forge a BSgenome data package” vignette): https://bioconductor.org/packages/BSgenome

• BSgenome software package on GitHub: https://github.com/Bioconductor/BSgenome

• Biostrings software package landing page: https://bioconductor.org/packages/Biostrings

• GenomeInfoDb software package on GitHub: https://github.com/Bioconductor/GenomeInfoDb