genus_species[_cultivar]/genus_species_version.fsa
Bacteria:
Fungi:
Metagenomes:
Data Files
- FASTA contigs, scaffolds, superscaffolds/chromosome (compressed)
- FASTQ Read files RAW data (compressed)
- Alignment files
- AGP Coordinate system translation
- Feature Format File
- Liftover
- Data registry metadata file (YAML)
- Common indices (bwa, bowtie2, blast, ...)
Naming conventions file names
Naming convention for entities
Patch files, patch scripts
BSGenome packages
Validators
Include a link to the validator for each format.
Genome Assembly
Naming Convention for Entities
Entities:
- Contig
- Scaffold
- superscaffolds/chromosome
- genes
Naming Convention for File Names
- fasta
- fastq
- alignment
- Feature Format File
- agp coordinate systems
Functional Annotation
Release Workflow
- save data in /output
- check naming conventions
- release
- add to the data registry
- add to ensembl
- data files on /output
- webapollo instance
- announce the release
\cite{embl-ebi}\cite{information}\cite{annotation}\cite{standards}\cite{pipeline}