Skip to content

Reference Genome

Reference Genome

Gencove offers access to the reference genome files utilized in generating project deliverables.

These files can be downloaded using the gencove projects get-reference-genome command. Alternatively, they are accessible through the web application, where you can download the genome.fasta file from the project detail page.

$ gencove projects get-reference-genome <project-id> <destination-dir>

Downloading subsets of deliverables

$ gencove projects get-reference-genome <project-id> <destination-dir> --file-types genome-fasta,genome-dict

Currently available file types are listed below (not all file types may be available for every project, please run gencove file-types --object reference-genome --project-id <project-id> for an accurate list of file types).

Reference genome sequence in FASTA format, compressed using gzip
Picard sequence dictionary corresponding to the reference genome sequence
Auxiliary file used by the BWA alignment tool for genome indexing
Annotation file used by the BWA alignment tool for genome indexing
Burrows-Wheeler Transform (BWT) index file, used for efficient sequence alignment
FASTA index file, providing quick access to sequences within the compressed FASTA file
Index file for the compressed FASTA file, facilitating quick retrieval of specific regions
Packed alignment data file used by BWA for indexing.
Suffix array file, a data structure used for pattern matching and genome alignment
Header file for a Variant Call Format (VCF) file, containing information about the reference genome and other metadata