PaSiT: a novel approach based on short-oligonucleotide frequencies for efficient bacterial identification and typing

Abstract

Motivation One of the most widespread methods used in taxonomy studies to distinguish between strains or taxa is the calculation of average nucleotide identity. It requires a computationally expensive alignment step and is therefore not suitable for large-scale comparisons. Short oligonucleotide-based methods do offer a faster alternative but at the expense of accuracy. Here, we aim to address this shortcoming by providing a software that implements a novel method based on short-oligonucleotide frequencies to compute inter-genomic distances. Results Our tetranucleotide and hexanucleotide implementations, which were optimized based on a taxonomically well-defined set of over 200 newly sequenced bacterial genomes, are as accurate as the short oligonucleotide-based method TETRA and average nucleotide identity, for identifying bacterial species and strains, respectively. Moreover, the lightweight nature of this method makes it applicable for large-scale analyses. Availability and implementation The method introduced here was implemented, together with other existing methods, in a dependency-free software written in C, GenDisCal, available as source code from https://github.com/LM-UGent/GenDisCal. The software supports multithreading and has been tested on Windows and Linux (CentOS). In addition, a Java-based graphical user interface that acts as a wrapper for the software is also available. Supplementary information Supplementary data are available at Bioinformatics online.

Assessing SARS-CoV-2 spatial phylogenetic structure: Evidence from RNA and protein sequences

“…Virotype 1 abundance was greater than expected in North America and smaller than expected in Europe and Asia. Virotypes 4,8,11,14,15,19,20,25,29,31,34,42,43,45 Phylogenetic structure analyses. The small dataset phylogeny is shown in Figure 2 structuring was highly significant for North America and Europe ( Table 1).…”

“…The fast distance method used here to analyze the large dataset produced results congruent with those obtained with the exact algorithm used to analyze the small dataset. Fast approaches similar to the one used here have already proven useful in previous virologic studies and high-throughput applications [23][24][25]. Further research is needed to determine the degree to which fast distance comparisons reflect actual similarities, especially if detailed mutational analyses are to be performed.…”

Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics

“…Sequencing was performed on the Illumina Novaseq 6000 platform using 2 × 150 bp paired-end sequencing by Baseclear, using their in-house pipeline (Leiden, The Netherlands). Selected bacterial strains were cultured and genomic DNA was extracted as outlined in [ 25 ]. Briefly, either a modification of the procedure of Pitcher et al .…”

“…PaSiT4, MMZ3, MMZ4 and Freq4. PaSiT4 is a parameter-dependent method based on tetranucleotide Karlin signatures that was originally optimized for inter-genome distances [ 25 ]. Here, it was implemented with a threshold (0.05) optimized for the selected fragment length following the same procedure as described in [ 25 ].…”

“…Sequencing was performed on the Illumina Novaseq 6000 platform using 2 × 150 bp paired-end sequencing by Baseclear, using their in-house pipeline (Leiden, The Netherlands). Selected bacterial strains were cultured and genomic DNA was extracted as outlined in [25]. Briefly, either a modification of the procedure of Pitcher et al [26], Gevers et al [27] and Wilson [28] or a Maxwell ® 16 Tissue DNA Purification Kit were used, after a prior enzymatic lysis step in case of gram-positive strains.…”