Scalable de novo classification of antibiotic resistance of Mycobacterium tuberculosis.

Motivation: World Health Organization estimates that there were over 10 million cases of tuberculosis (TB) worldwide in 2019, resulting in over 1.4 million deaths, with a worrisome increasing trend yearly. The disease is caused by Mycobacterium tuberculosis (MTB) through airborne transmission.

An Experimental Performance Assessment of Galileo OSNMA.

We present Galileo Open Service Navigation Message Authentication (OSNMA) observed operational information and key performance indicators (KPIs) from the analysis of a ten-day-long dataset collected in static open-sky conditions in southern Finland and using our in-house-developed OSNMA implementation. In particular, we present a timeline with authentication-related events, such as authentication status and type, dropped navigation pages, and failed cyclic redundancy checks. We also report other KPIs, such as the number of simultaneously authenticated satellites over time, time to first authenticated fix, and percentage of authenticated fixes, and we evaluate the accuracy of the authenticated position solution.

Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time.

A fundamental operation in computational genomics is to reduce the input sequences to their constituent k-mers. For maximum performance of downstream applications it is important to store the k-mers in small space, while keeping the representation easy and efficient to use (i.e.

Themisto: a scalable colored k-mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes.

Motivation: Huge datasets containing whole-genome sequences of bacterial strains are now commonplace and represent a rich and important resource for modern genomic epidemiology and metagenomics. In order to efficiently make use of these datasets, efficient indexing data structures-that are both scalable and provide rapid query throughput-are paramount.

Results: Here, we present Themisto, a scalable colored k-mer index designed for large collections of microbial reference genomes, that works for both short and long read data.

Matchtigs: minimum plain text representation of k-mer sets.

We propose a polynomial algorithm computing a minimum plain-text representation of k-mer sets, as well as an efficient near-minimum greedy heuristic. When compressing read sets of large model organisms or bacterial pangenomes, with only a minor runtime increase, we shrink the representation by up to 59% over unitigs and 26% over previous work. Additionally, the number of strings is decreased by up to 97% over unitigs and 90% over previous work.

Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time.

A fundamental operation in computational genomics is to reduce the input sequences to their constituent k-mers. For maximum performance of downstream applications it is important to store the k-mers in small space, while keeping the representation easy and efficient to use (i.e.

HaploBlocks: Efficient Detection of Positive Selection in Large Population Genomic Datasets.

Genomic regions under positive selection harbor variation linked for example to adaptation. Most tools for detecting positively selected variants have computational resource requirements rendering them impractical on population genomic datasets with hundreds of thousands of individuals or more. We have developed and implemented an efficient haplotype-based approach able to scan large datasets and accurately detect positive selection.

Syotti: scalable bait design for DNA enrichment.

Motivation: Bait enrichment is a protocol that is becoming increasingly ubiquitous as it has been shown to successfully amplify regions of interest in metagenomic samples. In this method, a set of synthetic probes ('baits') are designed, manufactured and applied to fragmented metagenomic DNA. The probes bind to the fragmented DNA and any unbound DNA is rinsed away, leaving the bound fragments to be amplified for sequencing.