Creating and managing sequence stores - AWS HealthOmics

Creating and managing sequence stores

HealthOmics sequence stores support storage of genomic files in the unaligned formats FASTQ (gzip-only) and uBAM, as well as the aligned formats, BAM, and CRAM. Imported files are stored as read sets, which are an AWS resource.This means you can add tags and control access through IAM. Aligned read sets require a reference genome to align genomic sequences, but it is optional for unaligned read sets.

To store read sets, you must first create a sequence store. When you create a sequence store, you can specify an optional Amazon S3 bucket as a fallback location. The fallback location is used for storing any files that fail to create a read set during a direct upload. Note that fallback locations are only available for sequence stores created after May 15, 2023. It is not possible to add a fallback location after the sequence store has been created.

aws omics create-sequence-store --name "MySequenceStore" --fallback-location "s3://DOC-EXAMPLE-BUCKET"

You receive the following response in JSON, which includes the ID number for your newly created sequence store.

{ "id": "3936421177", "arn": "arn:aws:omics:us-west-2:<account_ID>:sequenceStore/3936421177", "name": "MySequenceStore", "creationTime": "2022-07-13T20:09:26.038Z" "fallbackLocation" : "s3://DOC-EXAMPLE-BUCKET" }

You can also view all sequence stores associated with your account by using the list-sequence-stores command, as shown.

aws omics list-sequence-stores

You receive the following response.

{ "sequenceStores": [ { "arn": "arn:aws:omics:us-west-2:<account_ID>:sequenceStore/3936421177", "id": "3936421177", "name": "MySequenceStore", "creationTime": "2022-07-13T20:09:26.038Z" "fallbackLocation" : "s3://DOC-EXAMPLE-BUCKET" } ] }