SeqPanther: Sequence manipulation and mutation statistics toolset

Abstract

Pathogen genomes harbor critical information necessary to support genomic investigations that inform public health interventions such as treatment, control, and eradication. To extract this information, their sequences are analyzed to identify structural variations such as single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs) that may be associated with phenotypes of interest. Typically, this involves the assembly of reads, calling of variants, and calculation of a consensus sequence for downstream analysis. Several pipelines exist to perform quality control (QC) of raw reads and whole-genome assemblies. However, there is no easy-to-use, freely available bioinformatics QC tool to explore mappings for both positional codons and nucleotide distributions in mapped short reads of microbial genomes. To address this problem, we have developed a fast and accurate tool to summarise read counts associated with codons, nucleotides, and INDELs in mapped next-generation sequencing (NGS) short reads. The tool, developed in Python, also provides a visualization of the genome sequencing depth and coverage. Furthermore, the tool can be run in single or batch mode, where several genomes need to be analyzed. Our tool produces a text-based report that enables quick review or can be imported into any analytical tool for upstream analysis. Additionally, the tool provides the functionality to modify consensus sequences by adding, masking, or restoring to wild-type mutations specified by the user.

Rapid dynamic changes of FL.2 variant: A case report of COVID-19 breakthrough infection

“…We used SeqPanther [10] with the sequencing depth ≥1000, and minor allele frequency cutoff ≥1% to interrogate the intra-sample viral variant diversity between day-08 and day-21 sequences at genome positions known or strongly suspected to impact the transmissibility and immune evasiveness of SARS-CoV-2. For instance, the minority variant distributions in sequencing reads for the two time points at Spike positions P330, K417, G142, S373, and G667 significantly differed between the time points based on comparisons of proportions (p<0.05; Wilcoxon-Ranksum Test), Figure 1 b ; Supplementary Table 1.…”