Parsnp 2.0: Scalable Core-Genome Alignment for Massive Microbial Datasets

Abstract

Motivation:Since 2016, the number of microbial species with available reference genomes in NCBI has more than tripled. Multiple genome alignment, the process of identifying nucleotides across multiple genomes which share a common ancestor, is used as the input to numerous downstream comparative analysis methods. Parsnp is one of the few multiple genome alignment methods able to scale to the current era of genomic data; however, there has been no major release since its initial release in 2014.Results:To address this gap, we developed Parsnp v2, which significantly improves on its original release. Parsnp v2 provides users with more control over executions of the program, allowing Parsnp to be better tailored for different use-cases. We introduce a partitioning option to Parsnp, which allows the input to be broken up into multiple parallel alignment processes which are then combined into a final alignment. The partitioning option can reduce memory usage by over 4x and reduce runtime by over 2x, all while maintaining a precise core-genome alignment. The partitioning workflow is also less susceptible to complications caused by assembly artifacts and minor variation, as alignment anchors only need to be conserved within their partition and not across the entire input set. We highlight the performance on datasets involving thousands of bacterial and viral genomes.

Whole-genome analysis of Escherichia coli isolated from wild Amur tiger (Panthera tigris altaica) and North China leopard (Panthera pardus japonensis)

“…Whole genome data of some ST939 and ST10 strains were downloaded from NCBI for in-depth phylogenetic analysis with sequenced samples from this study. Parsnp 2.0.3 ( Kille et al, 2024 ) was used to identify single nucleotide polymorphisms (SNPs) in the E. coli genome set and to estimate a phylogenetic tree based on these SNPs. The evolutionary tree was constructed using RAxML 8.2.13 ( Stamatakis, 2014 ) with the maximum likelihood method and the bootstrap replication value was set to 1,000.…”