AutoBSgenome logoAutoBSgenome
Workflow guide · 01 / 03

How to use AutoBSgenome.

Search the package repository first. If the genome you need is not there, build a new one from NCBI or Ensembl and install the resulting tarball in R.

01

Search and download

Best when you need a common organism or want to avoid rebuilding an existing package.

  1. 01Open Packages and search by species, assembly, accession, or package name.
  2. 02Choose a matching package and inspect provider, assembly, source, and storage.
  3. 03Install from Bioconductor when available, or copy the AutoBSgenome one-line local install command.
Open search and download
02

One-click build

Best when you already have an NCBI accession or Ensembl species page.

  1. 01Open Build and paste an NCBI accession such as GCF_000001405.40, or an Ensembl species URL.
  2. 02Fetch metadata, check the generated package name and organism information, then submit the build.
  3. 03Wait for the job to finish, then download the temporary tarball or copy the one-line local install command.
Open one-click build
03

Manual review

Best when the metadata needs correction before the package is built.

  1. 01After metadata fetch, review package name, organism, common name, assembly, provider, and version.
  2. 02Check circular sequences, title, description, and source URL before starting the build.
  3. 03Use the generated result as the final installable source package for downstream R analysis.
Open manual review
Inputs

Common things users paste

AutoBSgenome accepts accessions, Ensembl pages, and package names depending on the page you are using.

  • NCBI RefSeq accessioninput · paste
    GCF_000001405.40

    Use this form for NCBI-hosted assemblies.

  • Ensembl species pageinput · paste
    https://www.ensembl.org/Danio_rerio/Info/Index

    Use this form when the genome is easier to identify from Ensembl.

  • Package searchinput · paste
    BSgenome.Hsapiens.NCBI.GRCh38

    Use this form when you already know the BSgenome package name.

Install in R

From a package card.

Install an AutoBSgenome-hosted package
R
local({options(timeout = 7200); url <- "TARBALL_URL"; tarball <- tempfile(fileext = ".tar.gz"); on.exit(unlink(tarball), add = TRUE); download.file(url, tarball, mode = "wb", method = "libcurl"); install.packages(tarball, repos = NULL, type = "source")})

Use the Copy button on a package card; it downloads the tarball first, then installs from a local file.

Install a Bioconductor-hosted package
R
BiocManager::install(
  "BSgenome.Hsapiens.UCSC.hg38"
)

Use this only for package cards labeled Bioconductor.

Recommended order

Search first. Build only if the package is missing. Then install the snippet shown by the browser or build result.

Start searching