Supernova1.0, printed on 08/12/2020
We describe here the input recommendations for Supernova 1.0. Because this initial version of Supernova has been tested primarily on human genomes, most of these recommendations are provisional, pending further experimentation and feedback from customers.
Genome size: Supernova has been tested on genomes in the size range 1.0-3.2 Gb.
Other genome characteristics: Supernova has not been tested on genomes having repeat content far greater than human, nor on genomes having extreme GC content.
Clonality: We strongly recommend that DNA be obtained from an individual organism or clonal population.
DNA size: We recommend that input DNA have size at least 50 kb. Larger DNA tends to produce assemblies with longer phase blocks and scaffolds.
Library generation: A single library should be generated, following the exact instructions for the Chromium system. For genomes of size 3.2 Gb, the recommended input mass is 1.25 ng. For genomes in the range 1.6-3.2 Gb, the input mass may be proportionally reduced, down to a minimum of 0.625 ng. Input mass should not be reduced further for smaller genomes.
Sequencing instrument: High quality Supernova assemblies have been obtained from reads generated on the HiSeq X and also the HiSeq 2500 (in rapid run mode). Other Illumina instruments may yield comparable results but have not been fully tested.
Read length: Supernova requires as input 2x150 base reads.
Sequencing depth: We recommend sequencing to depth between 38x and 56x. Within this range, higher coverage will generally give better results. For highly polymorphic organisms, we recommend 56x.