A comparison of short- and long-read whole-genome sequencing for microbial pathogen epidemiology | mSystems Genome assembly and variant calling are important steps in microbial population studies and epidemiology. Most variant calling and genotyping pipelines are designed for Illumina short sequencing reads...

Our manuscript comparing Nanopore vs. Illumina reads for population-level variant calling and genotyping is now out: journals.asm.org/doi/10.1128/... . This work was led by Andrea Schiffer and @arftrhmn.bsky.social.

Linear dicentric chromosomes in bacterial natural isolates reveal common constraints for replicon fusion | mBio Most bacterial genomes are monopartite with a single, circular chromosome. However, some species, like Agrobacterium tumefaciens, carry multiple chromosomes. Emergence of multipartite genomes is often...

Happy to share a new publication on a collaboration with Xindan Wang and @fuquaclay.bsky.social labs. We identified and characterized naturally occurring Agrobacterium strains with fused chromosomes. Did mobile genetic elements play a role in fusion? journals.asm.org/doi/10.1128/...

Please repost! and Save the date for the 13th Annual Yosemite Symbiosis Workshop (April 18-20, 2025).
More info at the registration page. REGISTRATION WILL OPEN SOON
www.sachslab.com/symbiosis-20...

Thank you!

I'm using MUMmer and MMSeqs for aligning (you have to preinstall them).

I have also used it for bacterial genome scale synteny visualization. Usually MUMmer is faster.

Future release will also have BLASTn implemented.

This is the first version. If anyone want to collaborate on this project, please let me know! I'm looking for testers, feature requests and bug reports will be appreciated!

Happy New Year 2025!

This is a Python based CLI. Since us, computational biologists, lives mostly in the terminal, having a quick utility to plot and play with synteny is a timesaver. If you use tool like `imgcat`, you can easily view the generated figures from the terminal, from your local computer or HPC.

There are some additional functionality in this tool to edit the input GenBank files -- so that you can customize the contig position, order, reverse-complement a particular contig in the GenBank file, etc.

You have to provide GenBank files for the genomes/contigs/plasmids that you want to visualize as well as an annotation file. It will align the GenBank files, find regions of similarity, and will plot the synteny.

I have released a command line tool for visualizing and annotating synteny plots called PySyntenyViz.

GitHub: github.com/acarafat/PyS...
PyPI: pypi.org/project/PySy...