DNA sequencing

All our genomic DNA projects are now sequenced using High-Fidelity (HiFi) mode resulting with up to 20 kb long HiFi reads with >99% read accuracy. We also offer CLR (continuous long read) sequencing for long libraries (30-40 kb) if needed. 

Please review DNA requirements section for information about DNA quality and amount needed. 

Hi-C library prep and sequencing

For reference genome projects run at our facility, we also offer Hi-C library prep and sequencing on NovaSeq. Currently we offer Hi-C library prep using Arima-HiCkit. 

 

What happens with my sample at NSC?

We always start with QC of the sample. This step includes clean-up with AMPure BP beads followed by spectrometry, Qubit measurement of DNA concentration and QC of integrity on Fragment Analyzer. It is common to lose up to 50% of input DNA during AMPure bead clean-up, therefore we recommend to send us more DNA than requested. You will be contacted if your sample does not pass our quality control. However, the final quality assessment of the DNA will be the single molecule sequencing process itself and you will always be charged for cost of sample QC, library preparation and sequencing of the library on one 8M SMRT cell. 

By default, all gDNA library preps include fragmentation of DNA using Megaruptor 3 and BluePippin size selection of the library. If input gDNA has short fragment length (mode >10kb but <20+ kb), we can start library preparation without fragmentation and will most likely still get good amount of data from sequencing. However, mean HiFi read length will be shorter than for input gDNA samples with fragment length >40-50 kb. 

After library prep, library is sequenced on number of SMRT cells requested. For multi-SMRT cell projects we always start with one SMRT cell, in order to confirm that the library sequences as expected. 

After sequencing has been finished, HiFi reads are generated using CCS pipeline. HiFi reads are then demulitplexed (amplicons, microbial samples, metagenomes and small genomes) and/or analyzed using PacBio software (e.g. Iso-Seq or Genome Assembly/Microbial Assembly).

Published Nov. 18, 2021 1:07 PM - Last modified Nov. 22, 2021 9:54 AM