Nina Dombrowski

Postdoc at the NIOZ and interested in microbial symbioses, extreme environments, metagenomics/genomes.

[antisense. @razoralign]

doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications https://t.co/3XUQ5yih4O

[Alain Tissier @trichomeIPB]

Attention! The IPB is looking for a new Head of Department in a joint appointment (W3 Professorship) with the University of Halle. This is an exceptional position. Come join us and shape the future of the IPB! https://t.co/0YYGzYJGH0

[Sarahi L. Garcia @sarilog]

Uni Oldenburg is starting a genomics facility, and we are looking for a bioinformatician.
https://t.co/oaF5vy6Qlf
The position is initially for 3 years, but there are chances of permanency after the 3 years.
Please share!

[Ryan Wick @rrwick]

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: https://t.co/NksiyESF7u
(1/5)

[Cameron Thrash @jcamthrash]

Engineering history with Asgard archaea of the kingdom Promethearchaeati https://t.co/4uCnSIfcPy

[Javier Santoyo @jsantoyo]

KEGG: biological systems database as a model of the real world. #KEGG @NAR_Open
https://t.co/1yibH6NZPO

[Johannes Köster (@johanneskoester.bsky.social) @johanneskoester]

There is a new #Snakemake tutorial that complements the general tutorial by specifically introducing how to use #Snakemake for plotting and interactive reporting, including how to combine #Snakemake with #Datavzrd: https://t.co/1mWPlOkcUY

[antisense. @razoralign]

GCI: A continuity inspector for complete genome assembly https://t.co/r4EgfQldL1

[antisense. @razoralign]

mulea: An R package for enrichment analysis using multiple ontologies and empirical false discovery rate https://t.co/bsuLo1eyfJ

[Ryan Wick @rrwick]

A little bit overdue, but here are my thoughts on @nanopore's recent release of Medaka:
https://t.co/SNYrZczPad

[Cameron Thrash @jcamthrash]

Strainy: phasing and assembly of strain haplotypes from long-read metagenome sequencing https://t.co/QN5SNJPwzi

[Cameron Thrash @jcamthrash]

CELEBRIMBOR: Core and accessory genes from metagenomes https://t.co/vTE9j07Vrb

[antisense. @razoralign]

SVbyEye: A visual tool to characterize structural variation among whole genome assemblies https://t.co/2DNwpdtDPW

[Gemma C Atkinson @gem__atkinson]

The ever amazing @art_egorov in our group has made a new visualisation tool for comparative genomics. Makes particularly beautiful images of phages, plasmids, other MGEs or regions of prokaryotic genomes 😍 https://t.co/Vk8FpS3NGX

[George Bouras @GB13Faithless]

Amazing and comprehensive guide to adding, updating and debugging bioinformatics software tools on Bioconda by @jfy133 (expanding on his earlier blogpost) - if you do bioinformatics software dev, it is truly all you need to get started with Bioconda

[Sarahi L. Garcia @sarilog]

Uni Oldenburg is starting a genomics facility, and we are looking for a bioinformatician.
https://t.co/jVVa8FCdxa
The position is initially for 3 years, but there are chances of permanency after the 3 years.
Please share!

[Michael Wagner @MichiWagner4]

A new substrate for #nitrification by #comammox microbes: #Guanidine

So glad to see this out in @Nature today – great collaborative effort from our @FWF Cluster of Excellence, @univienna, team @aalborg_uni, and @UFZ_de

https://t.co/devuSmLuix

[Bento Lab 🧬 @theBentoLab]

For anyone learning or teaching bioinformatics, or if you’re interested in getting started, you may like to check out some of many (>404!) detailed tutorials for the Galaxy bioinformatics platform, from microbiome analysis to chloroplast assembly, at https://t.co/633iyCPH2U 👇

The Galaxy platform is a free, easy-to-join, easy-to-use bioinformatics workflow management system that enables scientists to share, analyse and visualise their own data, without needing powerful computers and programming expertise.

Galaxy was first started in 2005, and it has grown year-on-year into an amazingly useful resource for scientists worldwide, with a global community of developers and end-users. You can read about it here:

The Galaxy Community. (2022). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic acids research, 50(W1).
https://t.co/mf3sUPa9LF

To get started, you could first go through a few tutorials to find out how the platform works at the following link:

https://t.co/3EimERhdk2

And you could take a look at some very cool tutorials, for example using Oxford @nanopore MinION data for:

⭐Analysing data to detect microbial pathogens such as Salmonella in food

https://t.co/gLuMqdhCWp

⭐Characterising the microbiome of beer

https://t.co/LKrxn5jJvB

⭐Diving into the bacterial biodiversity of soil

https://t.co/LPkNAuy7Ii

⭐Or assembling the chloroplast genomes of sweet potato and snow gum (Eucalyptus pauciflora) by combining Nanopore long read and Illumina short read data

https://t.co/HBGrmg8Mja

It also has tutorials for learning core skills in data science, such as using Python, bash, R, and SQL:

https://t.co/PHkZvcxTtp

Galaxy has a well-developed community, which you can find out more about here:

https://t.co/PgJvgdCQv6

And, if you have a particular application in mind, you might find a Galaxy pipeline that’s already been created as part of a published study. For example, if you’d like to find antimicrobial resistance genes in Salmonella, this article and workflow may be for you:

Lamas et al. (2023). Whole genome sequencing in the palm of your hand: how to implement a MinION Galaxy-based workflow in a food safety laboratory for rapid Salmonella spp. serotyping, virulence, and antimicrobial resistance gene identification. Frontiers in Microbiology, 14.
https://t.co/bs8LMrPNjY

Or if you’d like to find out how to produce a reference genome for a vertebrate as part of the Earth Genome project, this article explains how it can be:

Larivière et al. (2024). Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nature Biotechnology, 1-4.
https://t.co/bfHvOuWATn

All amazing resources for people already in the bioinformatics field, but possibly even more useful for teaching the bioinformaticians of the future!

This of course only covers a few aspects of the Galaxy “ecosystem”, so if it seems like it could be useful, be sure to have a look around and see what else there is out there for you.

And, if you are using Galaxy for teaching, we’d love to hear about how you’re using it, especially if you have any tips or online/published resources to share!

Disclaimer: Bento Lab has no affiliation with Galaxy - we just love cool tools and platforms that enable science!

[Cameron Thrash @jcamthrash]

MAGinator enables accurate profiling of de novo MAGs with strain-level phylogenies https://t.co/jKSjKE6ayX