Genetic variation among microbial strains of the same species can profoundly influence their phenotypes, ecological functions, and impacts on human health. Traditionally, the relative abundance of a s...

Changes Strobealign has been ported to Rust. The Rust version is at least as fast and accurate as the C++ version. There are currently some regressions due to the port: The Rust version cannot sat...

NUHS researchers use a genetic fingerprint to expose invisible microbial reservoirs, aiding outbreak prevention across local hospitals.

Free automated phage genome annotation -- pharokka, phold and phynteny in one pipeline.

Traditional methods for identifying associations between genomic features and traits, or between pairs of genomic traits, struggle when applied to bacterial genomes. While several microbial genome-wid...

a blog for miscellaneous bioinformatics stuff

The Great Barrier Reef Microbial Genomes Database compiles prokaryotic, viral and eukaryotic genomes from seawater collected from the Great Barrier Reef, providing a rich resource for the study of mar...

Existing notions of pangenome coordinates rely on hard-to-compute multiple sequence alignments. On the other hand, pangenome-wide exact unique matches (multi-MUMs) can be computed efficiently, and rep...

Posted 3:04:10 PM. Job DescriptionOur goal is to bring the widest benefits to society through enabling the analysis of…See this and similar jobs on LinkedIn.

Recently, Heng Li released MiniBWA (GitHub) alongside a paper by Heng Li and Nils Homer describing the method (paper). MiniBWA builds on the approaches in Minimap2 (also by Heng Li), but falls back on...

Most naturally occurring bacteria are lysogens, encoding one or more temperate phages (prophages) integrated into their genome. As prophages are induced by the bacterial SOS response, DNA-damaging ant...

Biological wastewater treatment relies on diverse microbial communities to degrade pollutants and drive nutrient transformations. Understanding the physiology and metabolism of these microorganisms is essential for improving the efficiency and cost-effectiveness of treatment processes. Much of our current knowledge is derived from 16S rRNA gene amplicon sequencing and metagenomic analyses. However, validating these sequencing- and genome-based insights requires bacterial species as pure cultures, and only a limited number of taxa common in wastewater treatment plants are currently available in culture. Here, we present an isolation strategy that uses antibiotics as a selective pressure to reduce microbial complexity and alleviate competitive exclusion during cultivation, while full-length 16S rRNA gene amplicon sequencing is used to monitor enrichment and guide targeted isolation, thereby facilitating the recovery of process-relevant activated sludge bacteria, including potentially uncultured taxa. These isolates can serve as model organisms for experimental validation of genome-based predictions.

4.0.0 (2026-06-12) ⚠ BREAKING CHANGES Replace anyhow with typed thiserror errors (#674) Change Phase conversion methods to use TryFrom for better error handling (#625) for pairwise alignment, only...

a blog for miscellaneous bioinformatics stuff

Folddisco enables protein structural motif search in million scale databases.

Prokaryotes harbor a diverse spectrum of extrachromosomal elements (ECEs), which are intracellular replicons maintained independently of the primary chromosome. Historically, the ECE research field ha...

Added #682 Added metacache classifier and improved nf-tests (added by @sofstam) #559 Profiling of long reads with motus (added by @LilyAnderssonLee and @sofstam ) #591 Add options to enable the ab...

Randomness is a powerful tool in the design and analysis of algorithms and data structures for nucleotide sequence data. Nucleotide sequences are not themselves random but are often randomized using hash functions. Despite their widespread use in genomics, there is no comprehensive review of the types of hash functions used and their various applications. In this survey intended for bioinformatic methods developers, we divide hash functions into four categories: scattering hash functions, permutations, minimum perfect hash functions, and locality-sensitive hash functions. For each category, we provide examples of both general-use hash functions that have been applied in nucleotide sequence analysis and hash functions that have been designed specifically for nucleotide sequence analysis. We highlight their salient properties, commonalities, differences, and application areas.

Overview We are pleased to release a metagenomic dataset from deep sequencing of a mature compost…

Nature - Telomere-to-Telomere Assembly Using HERRO-Corrected Simplex Nanopore Reads

sm-PORE-cupine combines SHAPE-based chemical probing with nanopore-based direct RNA sequencing to identify RNA structural ensembles in the SARS-CoV-2 genome and the Candida albicans transcriptome.

Abstract. Population-scale long-read DNA sequencing (PLRS) is rapidly reshaping our understanding of genomic variation in humans and non-model species. In

MIT - Computational Biology Program Scientist - Cambridge MA 02139