Search bioRxiv⌕ Search

Biology subjects

Lauris Kaplinski

Publications and source records attributed to Lauris Kaplinski.

2 recordsLinked to original sources
bioRxiv2016

FastGT: from raw sequence reads to 30 million genotypes in less than an hour

We have developed a computational method that counts the frequencies of unique k-mers in FASTQ-formatted genome data and uses this information to infer the genotypes of known variants. FastGT can detect the variants in a 30x genome in less than 1 hour using ordinary low-cost server hardware. The overall concordance with the genotypes of two Illumina \"Platinum\" genomes1 is 99.96%, and the concordance with the genotypes of the Illumina HumanOmniExpress is 99.82%. Our method provides k-mer database that can be used for the simultaneous genotyping of approximately 30 million single nucleotide variants (SNVs), including >23,000 SNVs from Y chromosome. The source code of FastGT software is available at GitHub (https://github.com/bioinfo-ut/GenomeTester4/).

Genomics↗
bioRxiv2016

StrainSeeker: fast identification of bacterial strains from unassembled sequencing reads using user-provided guide trees.

BackgroundFast, accurate and high-throughput detection of bacteria is in great demand. The present work was conducted to investigate the possibility of identifying both known and unknown bacterial strains from unassembled next-generation sequencing reads using custom-made guide trees.\n\nResultsA program named StrainSeeker was developed that constructs a list of specific k-mers for each node of any given Newick-format tree and enables rapid identification of bacterial genomes within minutes. StrainSeeker has been tested and shown to successfully identify Escherichia coli strains from mixed samples in less than 5 minutes. StrainSeeker can also identify bacterial strains from highly diverse metagenomics samples. StrainSeeker is available at http://bioinfo.ut.ee/strainseeker.\n\nConclusionsOur novel approach can be useful for both clinical diagnostics and research laboratories because novel bacterial strains are constantly emerging and their fast and accurate detection is very important.

Bioinformatics↗