Biology subjects

Puurand, T.

Publications and source records attributed to Puurand, T..

3 recordsLinked to original sources

bioRxiv2026

DIPLER: rapid k-mer-based locus identification

Here, we present Dipler, a two-step strategy that combines the identification of group-specific k-mers from whole-genome sequencing data with de novo assembly of PacBio reads enriched for those k-mers. Using a Gg/gg presence/absence-like model in Juglans hindsii, we recovered the structurally distinct "G" allele from PacBio reads at coverage as low as 9x. Using the exceptional GG genotype of J. regia "Sharkey" as a complementary diploid model, we further show that two divergent "G" alleles of the same locus can be resolved and assembled separately from 13x coverage. Dipler therefore provides a rapid, reference-independent framework for identifying structurally complex loci, with potential applicability across eukaryotic species.

bioinformatics↗

bioRxiv2020

KATK: fast genotyping of rare variants directly from unmapped sequencing reads

MotivationKATK is a fast and accurate software tool for calling variants directly from raw NGS reads. It uses predefined k-mers to retrieve only the reads of interest from the FASTQ file and calls genotypes by aligning retrieved reads locally. KATK does not use data about known polymorphisms and has NC (No Call) as default genotype. The reference or variant allele is called only if there is sufficient evidence for their presence in data. Thus it is not biased against rare variants or de novo mutations. ResultsWith simulated datasets, we achieved a false negative rate of 0.23% (sensitivity 99.77%) and a false discovery rate of 0.19%. Calling all human exonic regions with KATK requires 1-2 h, depending on sequencing coverage. AvailabilityKATK is distributed under the terms of GNU GPL v3. The k-mer databases are distributed under the Creative Commons CC BY-NC-SA license. The source code is available at GitHub as part of Genometester4 package (https://github.com/bioinfo-ut/GenomeTester4/). The binaries of KATK package and k-mer databases described in the current paper are available on http://bioinfo.ut.ee/KATK/.

bioinformatics↗

bioRxiv2019

AluMine: alignment-free method for the discovery of polymorphic Alu element insertions

BackgroundRecently, alignment-free sequence analysis methods have gained popularity in the field of personal genomics. These methods are based on counting frequencies of short k-mer sequences, thus allowing faster and more robust analysis compared to traditional alignment-based methods.\n\nResultsWe have created a fast alignment-free method, AluMine, to analyze polymorphic insertions of Alu elements in the human genome. We tested the method on 2,241 individuals from the Estonian Genome Project and identified 28,962 potential polymorphic Alu element insertions. Each tested individual had on average 1,574 Alu element insertions that were different from those in the reference genome. In addition, we propose an alignment-free genotyping method that uses the frequency of insertion/deletion-specific 32-mer pairs to call the genotype directly from raw sequencing reads. Using this method, the concordance between the predicted and experimentally observed genotypes was 98.7%. The running time of the discovery pipeline is approximately 2 hours per individual. The genotyping of potential polymorphic insertions takes between 0.4 and 4 hours per individual, depending on the hardware configuration.\n\nConclusionsAluMine provides tools that allow discovery of novel Alu element insertions and/or genotyping of known Alu element insertions from personal genomes within few hours.

genomics↗