How can library pools with samples of varying index lengths be sequenced on the AVITI and demultiplexed in Bases2Fastq? | Element Biosciences

Sequencing and demultiplexing library pools with samples that have index varrying index lengths can be accomplished two ways:

If all index sequences in a column on the run manifest are of the same length, sequence and demultiplex as normal. If all index sequences in a column differ in lenth, do one of the following:

• Use a single run manifest and append the first nucleotides of the adapter read next in sequencing to the end of shorter index sequences. This addition allows the shorter index sequences to match the length of the longest index sequence.
• Use multiple run manifests with different index sequence lengths, and execute Bases2Fastq multiple times. Make sure to update any impacted settings, such as base masks.

For detailed information, see Reconciling Different Index Sequence Lengths in the Run Manifest Online Help. https://docs.elembio.io/docs/run-manifest/example-samples/#reconciling