Dominik Buchner

🚨 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....

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...

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...

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

No, just regular 2 mL screwcap tubes.

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

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…

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…

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

The protocol is finally online:

protocols.io/view/co-extrac…

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

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

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?

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

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.

It's working 😍

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

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…

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 🤓

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!

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…

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

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

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

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

Check out GitHub for further information:

github.com/DominikBuchner…

#BOLDigger update: Asynchronous requests are now implemented into #BOLDigger speeding up the identification engine 2-4 fold, depending on internet connection and database availability. Up to 1000 sequences per hour are now possible! @leeselab

Release 1.3.6 released · DominikBuchner/BOLDigger Implemented an option to query the API of BOLD Systems for hits that have high similarity (>98%) but no species name assigned. The top hits have to be computed before the method can be run. Some...

Check the BOLDigger Github page for more information:

github.com/DominikBuchner…

GitHub - TillMacher/apscale_gui: Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data - TillMacher/apscale_gui

Available as a command-line version as well a GUI-version integrated by @TillMacher. Feel free to try it out and give us feedback on what options you would like to be added. #metabarcoding #pipeline #Bioinformatics

github.com/TillMacher/aps…

Check out our metabarcoding pipeline #apscale. Finally found the time to close the gap between my demultiplexing tool and #BOLDigger. Easy to install, option to run an all-in-one analysis from demultiplexed read to the OTU/ESV table. @leeselab

github.com/DominikBuchner…

All I want for Christmas is ~ 500 GB of raw read data or ~ 3.5 billion PE reads to demultiplex. #merrychristmas @leeselab #malaisetraps #bigdata