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Reposted by Dominik Buchner

Rudolf Meier @rudolf-meier.bsky.social · Mar 14

🚨 EntoSieve is now published in Molecular Ecology Resources: Fast and accurate size-sorting of bulk insect samples! Perfect for boosting DNA megabarcoding & metabarcoding projects. 🧬🔬 DIY low-cost device, gentle on specimens and yet efficient 🦋🐞 here: onlinelibrary.wiley.com/doi/full/10....

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Dominik Buchner @dominikbuchner.bsky.social · Feb 24

I just released version 3.0.0 of the upscale pipeline. It now implements optional replicate merging and the automatic removal of reads found in the negative controls. Check the details on my GitHub.
github.com/DominikBuchn...

Release 3.0.0 released · DominikBuchner/apscale

apscale can now automatically merge replicates and remove the maximum number of reads found in the negative controls the respective tab in the settings file has been added: 7_replicate_negative_con...

github.com

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Reposted by Dominik Buchner

Florian Leese @leeselab.bsky.social · Feb 21

Tolle #Biospektrum Ausgabe zu Hochduchsatzsequenzierung mit Review von @dominikbuchner.bsky.social & mir zu #Biodiversität #Monitoring mit #Metabarcoding
Wir betonen 3 besonders wichtige (& einfache) Schritte zur Qualitätssicherung & 4 nächste Schritte (nicht alle einfach).

tinyurl.com/ht-biodiv

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Dominik Buchner @dominikbuchner.bsky.social · Jan 31

No, just regular 2 mL screwcap tubes.

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Dominik Buchner @dominikbuchner.bsky.social · Jan 29

Just released version 1.6.0 of the APSCALE pipeline. This update includes improved log writing and added failsafe features for better handling of invalid settings. Check it out on GitHub:#apscale #metabarcoding #pipeline

github.com/DominikBuchner…

GitHub - DominikBuchner/apscale: Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data

Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data - DominikBuchner/apscale

github.com

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Dominik Buchner @dominikbuchner.bsky.social · Jan 29

We're happy to share our RNA cleanup protocol on @protocolsIO! Our method is significantly more cost-effective than commercial kits, without sacrificing effectiveness. Check it out here:#RNA #cleanup #openscience @leeselab

protocols.io/view/rna-clean…

RNA cleanup with magnetic beads

This protocol describes cleaning up RNA extracts with carboxylated magnetic beads and a PEG-NaCl buffer. It can also be used for volume reduction of a sample or buffer exchange...

www.protocols.io

Dominik Buchner @dominikbuchner.bsky.social · Jan 29

I hope my protocol will be a useful resource for the science community. I'm always looking for ways to give back, and I just wanted to say happy holidays to all of you. Merry Christmas! #merrychristmas #sciencecommunity #protocolsio

Dominik Buchner @dominikbuchner.bsky.social · Jan 29

The protocol is finally online:

protocols.io/view/co-extrac…

Co-extraction of RNA and DNA from soil and sediment samples

This protocol describes extracting RNA and DNA from soil and sediment samples. of soil or up to of sediment can be processed in one extraction. The protocol is based on the...

www.protocols.io

Dominik Buchner @dominikbuchner.bsky.social · Jan 29

Hint: Cleaning a phenol-contaminated centrifuge is not exactly a fun adventure. Avoid the hassle by taking good care when working with phenol-chloroform. Trust me, your labmates will thank you. #labtips #protocolsio 5/5

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Dominik Buchner @dominikbuchner.bsky.social · Jan 29

Our protocol is a reverse-engineered version of the RNeasy PowerSoil Total RNA Kit, but with a fraction of the cost. Our method reduces the cost from ~27€ per prep to ~6€, making it more accessible for researchers on a budget. #soilmicrobiology #RNA #costsaving #protocolsio 2/5

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Dominik Buchner @dominikbuchner.bsky.social · Jan 29

Twitter, your help is needed:
I'm desperately searching for small-volume, gravity-flow anion exchange columns comparable to the JetStar columns in the Qiagen RNeasy PowerSoil Total RNA Kit. Does anyone know a supplier for those columns?

Dominik Buchner @dominikbuchner.bsky.social · Jan 29

Soon the protocol will be added to my @protocolsIO. Still really hate working with phenol-chloroform but the result is worth the struggle.

Dominik Buchner @dominikbuchner.bsky.social · Jan 29

Co-extracting DNA/RNA from sediment haunted me for almost 2 years now with limited success so far. This changed today: I finally developed a protocol to process up to 15g of sediment in one extraction while splitting up DNA/RNA along the way. Will sleep like a baby tonight.

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Dominik Buchner @dominikbuchner.bsky.social · Jan 29

It's working 😍

Dominik Buchner @dominikbuchner.bsky.social · Jan 29

Sales representative:"How many plates do you need?"
Me:"Yes"
#upscaling

Dominik Buchner @dominikbuchner.bsky.social · Jan 29

Since everyone is talking about open science these days and I fully agree that knowledge should be accessible to anyone I will start putting all protocols I know on @protocolsIO. DNA extraction and bead cleanup are already up. Will add more gradually. 👨‍🔬🙂

protocols.io/researchers/m4…

Dominik Buchner on protocols.io

Metabarcoding, Genetics, Bioinformatics, Robotics

www.protocols.io

Dominik Buchner @dominikbuchner.bsky.social · Jan 29

Update on #BOLDigger: For the selection of any type of top hit all database entries containing punctuation and/or numbers will be ignored. This leads to cleaner taxa lists and less data cleaning needed for final analysis 🤓

Dominik Buchner @dominikbuchner.bsky.social · Jan 29

While producing similar results we were able to boost performance almost tenfold compared to other well known pipelines. APSCALE scales well with dataset size in terms of runtimes and ressources needed. Make sure to check out the benchmark!

Dominik Buchner @dominikbuchner.bsky.social · Jan 29

APSCALE is now published in Bioinformatics. Feel free to try out our metabarcoding pipeline, give feedback or tell us what to improve. Finally published sth in 2022 🥳💻@leeselab @TillMacherr

academic.oup.com/bioinformatics…

APSCALE: advanced pipeline for simple yet comprehensive analyses of DNA metabarcoding data

AbstractSummary. DNA metabarcoding is an emerging approach to assess and monitor biodiversity worldwide and consequently the number and size of data sets i

academic.oup.com

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Dominik Buchner @dominikbuchner.bsky.social · Jan 29

When the mainboard of your (real) computer is determined to commit suicide, so you are forced to spend the last weekend of your vacation backing up data and disassembling it. Good excuse to buy a new computer though 🥲🥲 #goodbyeoldfriend

Dominik Buchner @dominikbuchner.bsky.social · Jan 29

Updated BOLDigger and BOLDigger command-line to version 2.0.0. Selection of the top hit is now more sophisticated, check out the Readme for a detailed description of the function. Command-line version is now as quick and functional as the GUI. #BOLDigger #python #metabarcoding

Dominik Buchner @dominikbuchner.bsky.social · Jan 29

Started to work on automatic image annotation as a side project. Got serious quickly. Ordered an LED table and took photos with my cell phone. Works pretty well already, still need to add a scale to measure insects in mm instead of pixels 🤓#python #opencv #malaise @leeselab

Dominik Buchner @dominikbuchner.bsky.social · Jan 29

Time to learn some new (and hopefully exciting) stuff. I promise to stop using this as soon as I have my PhD. Good to know that this will still take a while 😁 #coding #ai #python

Dominik Buchner @dominikbuchner.bsky.social · Jan 29

Check out GitHub for further information:

github.com/DominikBuchner…

Release 1.4.0 released · DominikBuchner/BOLDigger

increased the request speed by more than 100% by using asynchronous coding. Depending on the internet connection the download speed of the results can be up to 4x as fast. Initial tests shows less ...

github.com