Corresponding authors: @ehauptfeld.bsky.social@bedutilh.bsky.social
IntegRATe your taxonomic profiling by downloading RAT ⏬ from github.com/MGXlab/CAT_p.... RAT is run with CAT_pack reads 🐀🐈⬛🦇. (5/5)
CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metagenomes - MGXlab/CAT_pack
Our study shows that by using this approach, RAT removes almost all falsely detected organisms in simulated data, and reduces the number of detected organisms in real metagenomic datasets by 80%! (4/5)
RAT largely removes this issue by rigorously prioritizing taxonomic signals by annotation reliability: Read maps to a MAG? -> assign to the same organism as the MAG. Read maps to an unbinned contig? -> same procedure. Only unmapped reads are annotated directly. (3/5)
Did you ever wonder why you can find Tree Lizard 🦎 DNA at the bottom of the ocean? Read-based shotgun metagenomics profiles notoriously include random species that have no business being in a sample. Reads are often short can therefore falsely match surprising organisms. (2/5)
The RAT is out! 🐀 Our new Read Annotation Tool integrates taxonomic signals from MAGs, contigs, and reads from #metagenomicswww.nature.com/articles/s41.... 🧵 (1/5)
Metagenomic taxonomic profiling usually relies either on reads or assembled contigs/MAGs. Here, authors present RAT, a tool that integrates taxonomic signals from reads, contigs, and MAGs into one pro...
Do you want to know which virus discovery tool to use? Check out @lingyi.bsky.social 's new paper:
#Viromics #VirusDiscovery 🦠 by #Metagenomics 🧬! We used real metagenomic data from diverse biomes to #benchmark state-of-the-art #bioinformatics virus identification tools: genomebiology.biomedcentral.com/articles/10.... @goncalopiedade.bsky.social @bedutilh.bsky.social 🧵 (1/4)
Background As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinfo...
#Viromics#VirusDiscovery#Metagenomics#benchmark#bioinformaticsgenomebiology.biomedcentral.com/articles/10....@goncalopiedade.bsky.social@bedutilh.bsky.social 🧵 (1/4)
Background As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinfo...
Excited to share the last chapter of #XinZhang'sbiorxiv.org/content/10.1...@binfutrecht.bsky.social#UUBeta#WesterdijkBiodiversity
Happy to see our most recent work on genome evolution of Fusarium isolates infecting banana published in @NewPhyt nph.onlinelibrary.wiley.com/doi/10.1111/...#AvWesterhoven@binfutrecht.bsky.social#UUBeta#WURplant#PhytoWUR@keygene.com