BS
AutoBSgenome
Workflow guide

How to use AutoBSgenome

Start by searching existing packages. If the genome you need is not available, build a new package from NCBI or Ensembl and install the resulting tarball in R.

Search and download
Best when you need a common organism or want to avoid rebuilding an existing package.
1

Open Packages and search by species, assembly, accession, or package name.

2

Choose a matching package and inspect provider, assembly, source, and storage.

3

Install from Bioconductor when available, or use the AutoBSgenome repository/download link.

Open search and download
One-click build
Best when you already have an NCBI accession or Ensembl species page.
1

Open Build and paste an NCBI accession such as GCF_000001405.40, or an Ensembl species URL.

2

Fetch metadata, check the generated package name and organism information, then submit the build.

3

Wait for the job to finish, then download the tarball or publish it to the repository.

Open one-click build
Manual review
Best when the metadata needs correction before the package is built.
1

After metadata fetch, review package name, organism, common name, assembly, provider, and version.

2

Check circular sequences, title, description, and source URL before starting the build.

3

Use 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 accession
GCF_000001405.40

Use this form for NCBI-hosted assemblies.

Ensembl species page
https://www.ensembl.org/Danio_rerio/Info/Index

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

Package search
BSgenome.Hsapiens.NCBI.GRCh38

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

Install from the package browser
Use this after you find an existing AutoBSgenome-hosted package.
install.packages(
  "PACKAGE_NAME",
  repos = "https://johnnychen1113.github.io/autoBSgenome"
)
Install a direct tarball
Use this after a build completes and you have a tar.gz URL.
install.packages(
  "https://example.org/BSgenome.Name_1.0.0.tar.gz",
  repos = NULL,
  type = "source"
)

Recommended order

Search first, build only if the package is missing, then use the install command shown by the package browser or build result. This avoids duplicate builds and keeps common packages easy to reuse.