Balancing read length and sequencing depth: Optimizing Nanopore long-read sequencing for monocots with an emphasis on the Liliales.

ABSTRACT:

Premise

We present approaches used to generate long-read Nanopore sequencing reads for the Liliales and demonstrate how modifications to standard protocols directly impact read length and total output. The goal is to help those interested in generating long-read sequencing data determine which steps may be necessary for optimizing output and results.

Methods

Four species of Calochortus (Liliaceae) were sequenced. Modifications made to sodium dodecyl sulfate (SDS) extractions and cleanup protocols included grinding with a mortar and pestle, using cut or wide-bore tips, chloroform cleaning, bead cleaning, eliminating short fragments, and using highly purified DNA.

Results

Steps taken to maximize read length can decrease overall output. Notably, the number of pore

SUBMITTER: De La Cerda GY 

PROVIDER: S-EPMC10278932 | biostudies-literature | 2023 May-Jun

REPOSITORIES: biostudies-literature