Reposted by Arafat Rahman
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.
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...
journals.asm.org
November 13, 2025 at 9:31 PM
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.
Reposted by Arafat Rahman
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/...
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...
journals.asm.org
May 20, 2025 at 2:37 PM
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/...
Reposted by Arafat Rahman
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...
More info at the registration page. REGISTRATION WILL OPEN SOON
www.sachslab.com/symbiosis-20...
January 30, 2025 at 8:18 PM
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...
More info at the registration page. REGISTRATION WILL OPEN SOON
www.sachslab.com/symbiosis-20...
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...
GitHub: github.com/acarafat/PyS...
PyPI: pypi.org/project/PySy...
January 8, 2025 at 9:25 PM
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...
GitHub: github.com/acarafat/PyS...
PyPI: pypi.org/project/PySy...