Sequencing

To submit a Sample for sequencing the user will specify how the Sample should be sequenced.

Sequencing Requests

To specify how a Sample is sequenced the user creates a Sequencing Request. A Sequencing Request identifies the source of material ( the Sample ), the type of sequencing data ( WGS, RNA-seq, etc ), and properties of the sequencing library ( what indices for demultiplexing ). Sequencing Requests go into a queue until they are ready to be filled.

Sequencing Runs

To collect sequencing data Sequencing Requests are pooled into collections of libraries that will be sequenced on the same Sequencing Run. Specifying the Sequencing Run configuration ahead of time can help with sequencing experiment design and avoid index collisions. After the sequencing experiment is specified the samples are loaded onto the sequencer and data is collected. When data collection is complete raw sequencing data is uploaded to s3. The raw sequencing data is demultiplexed to FASTQ files by linking the run archive with the Sequencing Run record and clicking the "Demultiplex" button. Indexing information from the Sequencing Requests is used to construct a SampleSheet used by bcl2fastq for demultiplexing, and run on AWS Batch.

Sequencing Data

On completion of demultiplexing FASTQ files are uploaded to s3 and records representing the FASTQ data (linking back to Samples, Attributes, and Groups) are indexed by SeqCMD.