Guides to improve your next generation sequencing project

read length, output and instrument recommendations for next generation sequencing

If you’re new to next generation sequencing or if you’re simply looking for tips to improve your next project, we recommend you take some time to look at the guides available on Genohub. As researchers order sequencing services it’s completely normal for there to be numerous questions related to nucleic acid extraction, library prep and best practices for loading a sequencing instrument. Over the years, we’ve curated these questions and published guides to help those embarking on their next NGS project. Topics covered include: library prep applications, batch effects, optimal cluster densities, read lengths and instrument output.

Next generation sequencing is a tool that can be applied to answer any number of questions related to the genome, transcriptome or epigenome. Regardless of the organism being sequenced or the library method used to prepare nucleic acid from that organism, the fundamentals of how a sequencing platform works, is similar across all samples. There are currently four main sequencing platforms that researchers regularly use. These include Illumina, Ion, PacBio and Oxford Nanopore. The guides below tend to be Illumina focused because that’s the platform most people are currently using today. Despite that, we review the read throughput of each available instrument and discuss hybrid methodologies where short and long reads are combined from two different instruments to improve assemblies.

Guides for sequencing

  1. Designing a sequencing project
  2. Recommended coverage by library preparation application
  3. Comparison of instrument read lengths and read outputs

Guides for preparing your samples

  1. Best practices for shipping tissue and nucleic acid 
  2. Library preparation kits and tips

Guides by application

  1. Transcriptome and mRNA-Seq
  2. Genome sequencing and re-sequencing
  3. Exome
  4. Metagenomics 
  5. Small RNA (microRNA)
  6. WGS vs. WES

Tips and considerations for commonly used sequencing instruments

  1. HiSeq X
  2. HiSeq 3000/4000
  3. Nextseq and low diversity

These are evolving guides, meaning our goal is to continuously improve them. If you have any feedback or would like to contribute please send us a message. We hope these guides will be helpful in designing your next NGS run. If you have technical questions related to an upcoming NGS project, feel free to submit them on our consultation page.

 

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