Oliver Schwengers 🇩🇪🇪🇺🇺🇦
@oschwengers1
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🦠🧬🖥️ Microbial bioinformatics, WGS bacteria, plasmids, PostDoc @JLUGiessen, father of 2, husband, astrophotographer
Giessen, Germany
Joined June 2019
Excited to share BakRep - our latest work published in @MicrobioSoc #MGen. >661,000 bacterial genomes, uniformly characterized & annotated, enriched with metadata, accessible via a flexible search engine. 👇 1/7.
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9th @denbiOffice "Microbial Genomics training course" now open for registration!. 3 sessions full of microbial bioinformatics at JLU Giessen:. I: QC & QA, assembly.II: regional & functional annotation.III: comparative genomics. Info & registration:
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To clarify and the sake of transparency: It is not a properly encrypted URL, but a base64-encoded ID + secret. So, if required, please use a proper encryption for URL sharing.
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And even without registration, results can easily and safely be shared with others using encrypted URLs. Of course, your data is handled with care automatically discarded after 30 days. Just give it a try: (5/5).
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Results are presented via a cross-referenced data table, a linear genome browser and circular genome plots - just choose your viz!. Of course, all results are also available for download in various standard file formats: GFF3, GenBank, EMBL, FASTA, TSV, TXT, JSON….(4/5).
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All executions are conducted in a scalable Kubernetes backend hosted within the @denbiOffice cloud. By this, Bakta Web dynamically scales out to meet temporal peak demands. (3/5).
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Bakta Web is our web application accompanying Bakta’s CLI version. It provides interactive widgets supporting users with both: the provision of input data and sample/sequence metadata, and the interpretation of annotation results. (2/5).
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We happily present: “Bakta Web – rapid and standardized genome annotation on scalable infrastructures” @OxUniPress NAR’s Web Server issue. Easy to use, no registration, fast, various visualizations, in sync with Bakta CLI:.(1/5).
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RT @cziscience: "Next generation Snippy will allow a detailed comparison of the world's bacterial genomes.” @torstenseemann & @wytamma are….
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Interested in bacterial genomes?. Hundreds of thousands, even millions?. All annotated, taxonomically classified, integrated with metadata. Easily searchable, viewable, downloadable, in sync with #AllTheBacteria. Then BakRep is for you!.Poster P-CM-102. @VAAM_Microbes #VAAM2025
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RT @shenwei356: Thrilled to finally debut my lab site 🎉: — which stands for Microbial Bioinformatics, a domain I pu….
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Of course, the DB light version was also updated, however DB sizes have barely changed. (6/6).
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This introduced a DB major scheme update from v5 to v6, which in turned resulted in a new software release v1.11.0:. (5/6).
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Due to this massive increase in known protein sequences, DB size has grown from 72GB to 83GB (deflated). To mitigate negative download effects for our users, we therefore switched compressions from gzip to xz. Compressed DB size actually decreased from 37GB to 30GB!. (4/6).
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To further improve annotation quality, external annotation sources have also been updated:. - COG: 2020 -> 2024.- Pfam: 36 -> 37.2.- RefSeq: r220 -> r228.- Rfam: 14.10 -> 15.- UniProtKB: 2023_05 -> 2025_01 . AMRFinderPlus and VFDB have been updated. (3/6).
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This is a massive increase in known protein sequences - which is great! . Numbers of IPS and PSC have grown by 22% and 13%. (2/6).
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🦠🧬🖥️ New Bakta DB v6.0 released!. After a year, it was time for a Bakta database update - and it's a huge one:. - IPS: 330.9M.- PSC: 135.3M.- PSCC: 37M. 👇 1/6.
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RT @VQuaschning: 2024 sind weltweit 6 Atomkraftwerke gebaut und 4 Atomkraftwerke stillgelegt worden. Macht ein Nettozubau von knapp 4 GW.….
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What a great 2025 binfie start!!!.
New year, new assemblies!.I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!.It's the successor to Trycycler, designed to be faster and less reliant on user intervention. Check it out: (1/5).
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RT @VQuaschning: In Frankreich geht nach 17 Jahren Bauzeit (12 Jahre länger als geplant) das #Kernkraftwerk Flamanville ans Netz. Die Koste….
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RT @ChrisStoecker: Eine Weihnachtskolumne: Kleiner Leitfaden für weihnachtliche Energiediskussionen mit Diesel-Dieter und Gas-Gertrud. Droh….
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