Creating and managing sequence stores
HealthOmics sequence stores support storage of genomic files in the unaligned formats of
FASTQ
(gzip-only) and uBAM
. It also supports the aligned formats of BAM
and CRAM
. Imported files are stored as read sets, which are an AWS resource. This means that you
can add tags and control access through IAM. Aligned read sets require a reference genome to align genomic
sequences, but it's optional for unaligned read sets.
To store read sets, you 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. Fallback locations are available for sequence stores created after May 15, 2023. You specify the fallback location when you create the sequence store. You can't add a fallback location after the sequence store is created.
In the following example, replace
with the
name you chose for your sequence store.sequence store name
aws omics create-sequence-store --name
--fallback-location "s3://DOC-EXAMPLE-BUCKET"
sequence store name
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-2:111122223333:sequenceStore/3936421177", "name": "sequence_store_example_name", "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 in the following.
aws omics list-sequence-stores
You receive the following response.
{ "sequenceStores": [ { "arn": "arn:aws:omics:us-west-2:111122223333:sequenceStore/3936421177", "id": "3936421177", "name": "MySequenceStore", "creationTime": "2022-07-13T20:09:26.038Z" "fallbackLocation" : "s3://DOC-EXAMPLE-BUCKET" } ] }
Additionally, you can use get-sequence-store to learn more about a sequence store by using its ID, as shown in the following.
aws omics get-sequence-store --id
sequence store ID
{ "arn": "arn:aws:omics:us-west-2:123456789012:sequenceStore/sequencestoreID", "creationTime": "2024-01-12T04:45:29.857Z", "description": null, "fallbackLocation": null, "id": "2015356892", "name": "MySequenceStore", "s3Access": { "s3AccessPointArn": "arn:aws:s3:us-west-2:123456789012:accesspoint/592761533288-2015356892", "s3Uri": "s3://592761533288-2015356892-ajdpi90jdas90a79fh9a8ja98jdfa9jf98-s3alias/592761533288/sequenceStore/2015356892/" }, "sseConfig": { "keyArn": "arn:aws:kms:us-west-2:123456789012:key/eb2b30f5-635d-4b6d-b0f9-d3889fe0e648", "type": "KMS" } }