Results of the Molecular Ecologist’s Survey on High-Throughput Sequencing

Some days ago, we asked our readers to fill in a survey (now closed) on your use of high-throughput sequencing techniques. We got a lot of responses, a total of 260 people filled in the form. Thank you! Here are the results of your answers.

Work in MEE

The great majority of respondents work with molecular ecology and/or evolution. There are also some that don’t necessarily work in these fields, but use sequencing methods.

Level

The majority of our readers are either graduate students or post docs. However, there are also many people in more senior positions, either with a professor title or somewhere around lecturer/associate prof/assistant prof. It’s very encouraging to see that there are interest from people encompassing all different levels.

What kind of organism(s) do you study? (your main project only)

organism

This is interesting: most of our readers study some kind of plant! Go plants! Plants encompasses an entire kingdom, so is of course a very big and species-rich group, but with that logic, bacteria should win as they make up an entire domain. Mammals come as a strong second contender, followed by fish, insects, and birds. Overall, TME’s readers study a very diverse set of organisms. There is not a huge bias towards one group of organisms, like one could imagine with mammals since they include our own species. Indeed, fungi, viruses and eukaryotic microbes are represented too. Perhaps the diverse set of organisms reflect that many readers study ecology?

4.usage

The great majority of our readers use high-throughput sequencing (HTS) methods extensively, and almost everyone else either use them a little bit, or plan to use them. Only 1.6% people answered that they are not using HTS. It’s very positive to see that the molecular ecologists are not afraid to keep up with new molecular methods and follow the modern sequencing techniques. Disclaimer: since this survey was created around the topic of HTS, it is likely that we attracted responses primarily from people using these methods, and that people not using them were less likely to respond. With this in mind, we continue to look at the results from the questions that were available only to the people who did use or will use HTS.

5.own_machines

Most people do not have access to any HTS machine at their workplace. This would mean that most labs send away their samples for sequencing somewhere else. Some people have access to one, two, or three machines, but only 10% have local access to several.

What sequencing technology are you mainly using?

seq_tech

Not surprisingly, the overwhelming majority currently use Illumina technology when sequencing, especially HiSeq and MiSeq that have been around for a while now. NextSeq is still somewhat new (2 years) and the MiniSeq is likely too new for this survey (~2 months). There are a few people that use the new and upcoming machines from Oxford Nanopore and PacBio. And some still use older techniques, such as 454, though it is possible many of these respondents have used 454 data in their project and are now transitioning to new sequencers. Data from 454 is still very much useful, despite the machines being discontinued.

What do you sequence?
sequence_what

When it comes down to what people are sequencing, reduced representation of genomes and whole genomes are preferred. It is interesting to see that methods such as RAD-seq, highly targeted to the field of molecular ecology and population genetics, are so popular among our readers. Seeing as HTS is still relatively expensive when you have a lot of samples, reduced representation of genomes can be a good way to e.g. resolve phylogenetic relationships. In third place we find transcriptomes, followed by sequence capture and amplicon sequencing.

7.ref_genome

Almost half of the respondents do not have any current reference genome available (43%). And 37% have only a partial genome or a reference for some of their study species. These answers likely reflect the fact that many molecular ecologists work with wild and non-model organisms.

Who is collecting the samples in your main project? (field work or lab work)

collecting_samples

Who is doing the wet lab processing of samples in your main project? (DNA extraction and library preparation)

lab_work

When it comes down to collecting samples, doing DNA extraction and library preparation, two thirds of the readers perform such tasks themselves, many with help from colleagues and lab/field assistants. I find it interesting that quite many people responded that the public or museums collect samples. Does that mean that museum samples are often used for sequencing, or that citizen science is more common than I thought?

Who is doing the bioinformatic analyses in your main project?

bioinformatics

A staggering 89% of all readers answered that they themselves perform the bioinformatic analyses. This is very useful for the TME crew to know, as we can now write about bioinformatic analyses without wondering too much if we will be targeting only a tiny niche of interested readers. A third of the readers also have help from lab colleagues (this broad category included all levels: students, postdocs, PIs and other employees of e.g. PIs).

hts_interest

Finally, most readers do want to read about sequencing methods, bioinformatic analyses, and studies utilizing HTS. This is highly encouraging for the Molecular Ecologist, and we will do our best to continue deliver articles within these topics. Thank you again to all of those who filled in the survey! Any thoughts about the results? Please leave a comment!

 

Images in this post: Pie charts were automatically generated by Google Forms. The bar charts were made by me in R using ggplot2.

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About Elin Videvall

Elin is a PhD candidate in the Molecular Ecology and Evolution Lab, Lund University, Sweden. She studies birds and their microbes by analysing genomes, transcriptomes, and microbiomes. You can find her on Twitter: @ElinVidevall
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