Dominik Buchner
@dominikbuchner.bsky.social
Staff reasearcher at @leeselab.bsky.social
studying molecular biology, bioinformatics, and robotics. Developing tools to democratize molecular biology.
studying molecular biology, bioinformatics, and robotics. Developing tools to democratize molecular biology.
Reposted by 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....
March 14, 2025 at 3:03 PM
🚨 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....
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...
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
February 24, 2025 at 10:34 AM
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...
github.com/DominikBuchn...
Reposted by Dominik Buchner
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
Wir betonen 3 besonders wichtige (& einfache) Schritte zur Qualitätssicherung & 4 nächste Schritte (nicht alle einfach).
tinyurl.com/ht-biodiv
February 21, 2025 at 9:34 AM
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
Wir betonen 3 besonders wichtige (& einfache) Schritte zur Qualitätssicherung & 4 nächste Schritte (nicht alle einfach).
tinyurl.com/ht-biodiv
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.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
January 29, 2025 at 1:38 PM
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.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…
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
January 29, 2025 at 1:38 PM
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…
protocols.io/view/rna-clean…
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?
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?
January 29, 2025 at 1:38 PM
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?
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?
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.
January 29, 2025 at 1:38 PM
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 😍
January 29, 2025 at 1:37 PM
It's working 😍
January 29, 2025 at 1:37 PM
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…
protocols.io/researchers/m4…
Dominik Buchner on protocols.io
Metabarcoding, Genetics, Bioinformatics, Robotics
www.protocols.io
January 29, 2025 at 1:37 PM
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…
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 🤓
January 29, 2025 at 1:37 PM
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 🤓
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…
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
January 29, 2025 at 1:37 PM
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…
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
January 29, 2025 at 1:37 PM
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
January 29, 2025 at 1:37 PM
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
January 29, 2025 at 1:37 PM
#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
January 29, 2025 at 1:37 PM
#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
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…
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
January 29, 2025 at 1:36 PM
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…
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
January 29, 2025 at 1:36 PM
All I want for Christmas is ~ 500 GB of raw read data or ~ 3.5 billion PE reads to demultiplex. #merrychristmas @leeselab #malaisetraps #bigdata
It took me 9 full working days to extract 3316 Malaise Trap samples. Lessons learned: Sleep is not that important. Maybe it's time to scale down. I need to lose some (more) weight. 36 plates of PCR incoming. @leeselab #upscaling #insectmonitoring #metabarcoding
January 29, 2025 at 1:36 PM
It took me 9 full working days to extract 3316 Malaise Trap samples. Lessons learned: Sleep is not that important. Maybe it's time to scale down. I need to lose some (more) weight. 36 plates of PCR incoming. @leeselab #upscaling #insectmonitoring #metabarcoding
In our new study, we show how to automatize metabarcoding pipelines on liquid handlers. We used two datasets to demonstrate the high reproducibility and robustness of our workflow. Great to finally see this paper published! 🙃🧑🔬🧬🕹️@leeselab @TillMacher
sciencedirect.com/science/articl…
sciencedirect.com/science/articl…
January 29, 2025 at 1:36 PM
In our new study, we show how to automatize metabarcoding pipelines on liquid handlers. We used two datasets to demonstrate the high reproducibility and robustness of our workflow. Great to finally see this paper published! 🙃🧑🔬🧬🕹️@leeselab @TillMacher
sciencedirect.com/science/articl…
sciencedirect.com/science/articl…
Finally, we have not one but four!!! 96-well gel chambers 😍🧑🔬@leeselab #upscaling
January 29, 2025 at 1:36 PM
Finally, we have not one but four!!! 96-well gel chambers 😍🧑🔬@leeselab #upscaling
Looking for a cheap and efficient way to homogenize invertebrate bulk samples?! We developed a cheap and time-saving homogenization and cleaning protocol using a common kitchen blender. 🧑🔬🧬 #upscaling #metabarcoding @pipette_jockey @leeselab
mbmg.pensoft.net/article/67533/
mbmg.pensoft.net/article/67533/
January 29, 2025 at 1:36 PM
Looking for a cheap and efficient way to homogenize invertebrate bulk samples?! We developed a cheap and time-saving homogenization and cleaning protocol using a common kitchen blender. 🧑🔬🧬 #upscaling #metabarcoding @pipette_jockey @leeselab
mbmg.pensoft.net/article/67533/
mbmg.pensoft.net/article/67533/
Scaling down metabarcoding PCRs to uL is totally fine. Considerable reduction of costs and downstream chemicals :). First paper for 2021 out. #downscaling @leeselab
onlinelibrary.wiley.com/doi/10.1002/ec…
onlinelibrary.wiley.com/doi/10.1002/ec…
Cooking small and large portions of “biodiversity‐soup”: Miniaturized DNA metabarcoding PCRs perform as good as large‐volume PCRs
In this study, we tested the influence of PCR volume on bulk sample metabarcoding outcomes. Our results show that neither species richness nor replicate consistency is systematically influenced by PC...
onlinelibrary.wiley.com
January 29, 2025 at 1:36 PM
Scaling down metabarcoding PCRs to uL is totally fine. Considerable reduction of costs and downstream chemicals :). First paper for 2021 out. #downscaling @leeselab
onlinelibrary.wiley.com/doi/10.1002/ec…
onlinelibrary.wiley.com/doi/10.1002/ec…