Library Preparation Guide

One of the most important steps in the sequencing process is library construction. With the rapid expansion of Next Generation Sequencing into a growing number of labs, the number of techniques to create libraries has grown. Heard or Gro-Seq, HITS-CLIP or GBS? These are just a few examples of established techniques that took on a sequencing twist (genomic run-on, cross-linking immunoprecipitation and genotyping respectively). You could say that the growing throughput of sequencing has enabled these methods and that these methods are enabling the growth of sequencing into more labs. Our aim is to keep track of these techniques, offer brief descriptions of each, along with comparison metrics. We’ve started by writing the Guide to Library Preparation, describing the techniques and kits used by our service providers on Genohub. When searching for library preparation services on Genohub, researchers will be able to see the type of kit a provider uses and click on its name for a more detailed description of the technology behind the construction of libraries.

As of today, there are a little more than 200 different techniques to construct libraries. Our guide is certainly a work in progress. If you’ve recently developed a new technique and would like it described in our guide, please contact us with a description of the library protocol. We’re also looking for feedback on the guide’s content and what you think we should add.

8 Top Online Calculators for Next Gen Sequencing

When it comes to next gen sequencing, here are the top 8 online calculators that we have found:

Coverage

  1. Genohub’s shop by project feature
  2. The Coverage Calculator by Clinical Genomics

Oligonucleotide

  1. The Oligo Calc: Oligonucleotide Properties Calculator by Northwestern University
  2. The OligoAnalyzer 3.1 by Integrated DNA Technologies

Primers

  1. NCBI/ Primer-BLAST: Finding primers specific to your PCR template (using Primer3 and BLAST) 
  2. Primer3: WWW primer tool by UmassMed

qPCR Efficiency

  1. The qPCR efficiency calculator by Thermo Scientific
  2. The QPCR Standard Curve Slope to Efficiency Calculator by Agilent Technologies

If you know of any other great online calculators for next gen sequencing please tell us about it!

Targeted Resequencing (TPS/WES) Tops Next Gen Sequencing Survey

Oxford Gene Technology (NGS provider currently listed on Genohub) recently presented the results of their next gen sequencing survey which demonstrated targeted resequencing as the top use for next generation sequencing. The results are based on a survey of 596 researchers who responded regarding their current and expected use of NGS services. When compared to the results for whole genome sequencing the popularity of targeted resequencing is possibly attributed mostly to the lower cost of targeted resequencing. This infographic depicts the results:

OGT NGS Survey Results

OGT NGS Survey Results

Other interesting results point to a general data problem with 38% of respondents saying they lack trust in bioinformatics data. Bioinformatics also leads the field when researchers were asked about the biggest barrier to NGS usage (see below).

Barriers to NGS Usage

Barriers to NGS Usage

Undoubtedly this presents an immense opportunity for the bioinformatics sector to increase confidence in data accuracy and interpretation which could have a positive impact on the use of next gen sequencing as a whole.

You can find many more interesting survey results on the excellent infographic titled Oxford Gene Technology – NGS Survey 2013.