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Ensembl GenomIO

A repository dedicated to pipelines used to turn basic genomic data into formatted Ensembl core databases. Also allow users to dump core databases into various formats.

File formats handled : FastA, GFF3, JSON (following BRC4 specifications).

Contents

Check out installation section for further information on how to install the project.

  1. Install
  2. Usage
  3. Code of Conduct
  4. Code reference

Ehive pipelines

Check out the usage section for further information of requirements to run ensembl-genomio pipelines.

  1. Genome loader: Creates an Ensembl core database from a set of flat files.
  2. Genome dumper: Dumps flat files from an Ensembl core database.

Nextflow pipelines

  1. Additional seq prepare: BRC/Ensembl metazoa pipeline. Preparation of genome data loading files for new sequence(s) to existing species databases.
  2. Genome Prepare: BRC/Ensembl metazoa pipeline. Retrieve data for genome(s), obtained from INSDC and RefSeq, validate and prepare GFF3, FASTA, JSON files for each genome accession.

License

Software as part of Ensembl GenomIO is distributed under the Apache-2.0 License.