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Quality filtering metabarcoding datasets!

When dealing with metabarcoding data, we typically cluster sequences by similarity into operational taxonomic units (OTUs), as sequences are affected by sequencing errors. However, just clustering sequence data will not be efficient without pre filtering data e.g. remove low quality… Continue Reading →

Nanopore is on fire!

That nanopore sequencing read quality will have to be improved substantially (~10%-15% errors with earlier versions) is obvious, and nanopore has just done that (video) a few month ago with improved pores and base calling algorithms. But when I looked on twitter… Continue Reading →

Using the Biomek FXp for DNA barcoding!

The pride of the leselab is our pipetting robot Biomek FXp from Beckman Coulter, which arrived earlier this year. Together with a team from Beckman Coulter we are currently setting it up for our high trough put sequencing and sample processing pipelines. The first big… Continue Reading →

New PrePrint: Testing 16S for DNA metabarcoding!

I’m really a COI guy when it comes to aquatic invertebrates: good references and species level resolution. However, there is a small but vocal community pushing the ribosomal marker 16S for DNA metabarcoding. The advantage is clear; highly conserved gene regions wich should be… Continue Reading →

How much ng DNA do you need for insect DNA (meta)barcoding?

To copy a target DNA fragment with Polymerase chain reaction (PCR), typically 1-150 ng Template DNA is used in the reaction (see e.g. 5Primer HotMaster Taq manual). We use the Cytochrome c oxidase subunit I (COI) barcoding gene to identify hundreds… Continue Reading →

The high throughput sequencing black box

The field of high throughput sequencing (HTS) is rapidly evolving, making it is almost never worth it for an university to buy a HTS device like illumina sequencers. While this might change in the future when prices further decline, sending your… Continue Reading →

Why I’m done with PlosONE!

My supervisor an I published our first DNA metabarcoding manuscript in PlosONE this year, demonstrating influence of primer bias and taxa biomass. The paper is doing quite well, and I’m quite happy with it. However, what remains hidden to the reader is all… Continue Reading →

Why the Bento Lab is a big deal!

A few month ago I spotted pictures of the Bento Lab on twitter, a compact suitcase sized mini PCR lab for the field. My first thought was: “Cool, I need one!” and the second one: “What could you do if you combine… Continue Reading →

Why the Clear Food’s hot dog report is flawed and misleading!

The label on our food does not always reflect the what is in a product. This became very clear in Europe in 2013 were horse meat was found in many frozen meat products, without this component being declared on the package…. Continue Reading →

DNA Metabarcoding vs. Metagenomics

I was at the Science for the Environment conference in Aarhus (Denmark) last week, which focussed 3 days on new trends and developments in the biodiversity monitoring community. It was really cool to see how remote drones are now used in monitoring, especially for… Continue Reading →

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