Updates for March 2024
Updates for March 2024
Vedanth & Anna visit Brisbane
Looking forward to the next quarter. Luis will hold two Zoom open office hours sessions, at two very different times of the day: (i) April 24 in the Australian morning (which is the evening of the previous day in the US) and (ii) May 9 in the evening (morning in Europe).
Focus of the Quarter: argNorm, Vedanth’s Project
Antimicrobial resistance (AMR) is a major public health challenge with global impact. With EMBARK and now SEARCHER, we have been looking at how antibiotic resistance is spread, including in host-associated and environmental microbiomes. This month we focus on Vedanth Ramji, who has been working on argNorm along with Svetlana and others.
What is argNorm? There are many bioinformatics tools that identify antimicrobial resistance genes (ARGs), each using different methods and output formats. The hAMRonization package normalizes the file formats, but that still leaves the issue that different tools will use different vocabularies (e.g., calling the same gene TETX, or Tet-X, or Tet(X), which causes problems for automated processing). To address this, we developed argNorm: a command line tool and a Python library to normalize ARG annotation from 5 different ARG annotation tools.
argNorm maps the outputs of ARG annotation tools to a common vocabulary, namely the antibiotic resistance ontology (ARO) developed by the Comprehensive Antibiotic Resistance Database (CARD). The ARO provides unique identifiers (ARO numbers) for each gene. Through this, we hope to facilitate reliable and convenient comparisons of ARG annotation tools and gain a deeper understanding of ARGs in genomes and metagenomes.
More information: argNorm video Tutorial
Could you tell us a bit about yourself, Vedanth? I am a high-school senior at APL Global School in Chennai, India. I learned programming in middle-school through creative coding. After self-studying high-school biology, I joined Queromatics, a cancer NGO in the US, as a software development intern. I then enrolled in a college-level research program in bioinformatics. This led me to join the Big Data Biology Lab. After high-school, I hope to attend a rigorous undergraduate program where I can combine my passion for math, biology, computer science and engineering.
Where can people find you and get in touch? Here is my email: vedanth.ramji@gmail.com. I am also on LinkedIn: https://www.linkedin.com/in/vedanth-ramji/
People.
Vedanth and Anna are currently visiting the lab in Brisbane. Anna presented her postdoc work on long-read metagenomics of Shanghai pet dogs internally at the Center of Microbiome Research. Vedanth is visiting through a grant from Emergent Ventures India.
Manuscripts.
Marija’s paper A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer (HGT) is now out at Nature Ecology & Evolution describing how HGT events in the distant past differ from the more recent ones (and more).
We published a review (Challenges in computational discovery of bioactive peptides in ’omics data) in Proteomics where we argue that large (meta)genomics resources represent a large opportunity for mining peptides, but the methods that work for canonical-length proteins do not work for short ones.
Luis’ perspective For long-term sustainable software in bioinformatics is available in PLOS Computational Biology. This piece actually grew out of the June 2022 newsletter, where we discussed our tools and that we have maintained them for several years. This led to some social media discussion, and eventually to this piece.
Software tools.
strobealign v0.13.0: We have been working with the strobealign developers to make it even better and v0.13 incorporates some of that work, including very fast coverage estimates, which can be used by SemiBin!
SemiBin v2.1 can use the very fast coverage estimates from strobealign v0.13 to bin faster.
argNorm v0.2 updated all the mapping to the ARO (antibiotic resistance ontology) and added drug class categorization to outputs.
mahotas v1.4.14 is out. This updates the package for C++17
Other.
The Extremely Open Science project posted several streams and updates on our YouTube channel.
Alumni news.
Congratulations to Célio for having gotten a Marie Skłodowska-Curie Fellowship to work at ICM in Barcelona on environmental microbiome dynamics over time.