July 2024 - Bioinfo List - SeqShare Mailing Lists

Yet another AMR pipeline: AMRomics
by Marco van Zwetselaar 31 Jul '24

31 Jul '24

AMRomics: a scalable workflow to analyze large microbial genome collections https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-10620-8 Two interesting features (vis a vis other pipelines): support for Nanopore reads, and construction of phylogenetic trees from core-genomes of the data. Cheers, Marco

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Reminder: Bioinformatics COP this Thursday!
by Christa Twyford Gibson 30 Jul '24

30 Jul '24

Dear Colleagues, Don't forget this month's SeqAfrica Bioinformatics Community of Practice meeting! We will be discussing new developments in sequencing and bioinformatics tooling for microbial / AMR genomics. The meeting is Thursday (1.8.24) at 14:00 CEST. The zoom link is below. We can't wait to see and hear from you! Please share this invitation with your bioinformatics-curious and interested friends! Kind Regards, Christa Join Zoom Meeting https://dtudk.zoom.us/j/68365887835 Meeting ID: 683 6588 7835 [cid:image001.png@01DAE276.7B716BE0] Christa Twyford Gibson Project Manager for SeqAfrica Project SEQAFRICA (antimicrobialresistance.dk)<https://antimicrobialresistance.dk/seqafrica.aspx> chrgi(a)dtu.dk<mailto:chrgi@dtu.dk> +45 935 106 61 National Food Institute Research Group for Global Capacity Building Building 204 Henrik Dams Allé 2800 Kgs. Lyngby www.food.dtu.dk<http://www.food.dtu.dk/>

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... and yet another plasmid finder
by Marco van Zwetselaar 30 Jul '24

30 Jul '24

PlasmidHunter: accurate and fast prediction of plasmid sequences using gene content profile and machine learning https://doi.org/10.1093/bib/bbae322 Cheers, Marco

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BLAST core_nt to be default from Aug 1st
by Marco van Zwetselaar 24 Jul '24

24 Jul '24

NCBI announces the "better, faster, smaller" core_nt database to become the default from August: From: NLM/NCBI List blast-announce [<blast-announce(a)ncbi.nlm.nih.gov>](mailto:blast-announce@ncbi.nlm.nih.gov) Interested in faster nucleotide BLAST searches with more focused search results? NCBI has been re-evaluating the BLAST nucleotide database (nt) to make it smaller and more efficient. Thanks to your feedback, we have created the core nucleotide database (core_nt), an alternative to the default nt database that contains better-defined content and is less than half the size. Read more at NCBI Insights and try out the new database: https://bit.ly/46d49r8 https://bit.ly/46d49r8

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Benchmarking short and long read polishing tools for Nanopore assemblies
by Marco van Zwetselaar 17 Jul '24

17 Jul '24

Thorough evaluation of Nanopore assembly polishers: Benchmarking short and long read polishing tools for nanopore assemblies: achieving near-perfect genomes for outbreak isolates https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-10582-x Best wishes, Marco

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Reminder: SeqAfrica Bionformatics Community of Practice this Thursday at 14:00 CEST
by Christa Twyford Gibson 02 Jul '24

02 Jul '24

Dear Colleagues, We are looking forward to the next commiunity of practice session to take place this Thursday at 14:00 CEST! We will have a special guest host, Niamh Lacy-Roberts, who will discuss the results of SeqAfricas's recent optimization experiments for ONT sequencing. In particular, she will cover testing various input concentrations and multiplexing different numbers of isolates using the rapid barcoding kit. The focus of the experiments was to determine the best combination that yields the highest sequence quality, enabling accurate typing (MLST, AMR genes etc) and cluster analysis. She will also go over the tools used to analyze the ONT data. You can join the meeting here: Join Zoom Meeting https://dtudk.zoom.us/j/68365887835 Meeting ID: 683 6588 7835 We look forward to seeing you Thursday! Kind Regards, Christa [cid:image001.png@01DACC7E.F37D4630] Christa Twyford Gibson Project Manager for SeqAfrica Project SEQAFRICA (antimicrobialresistance.dk)<https://antimicrobialresistance.dk/seqafrica.aspx> chrgi(a)dtu.dk<mailto:chrgi@dtu.dk> +45 935 106 61 National Food Institute Research Group for Global Capacity Building Building 204 Henrik Dams Allé 2800 Kgs. Lyngby www.food.dtu.dk<http://www.food.dtu.dk/>

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2025

2024

Bioinfo List July 2024