HashSeq: a Simple, Scalable, and Conservative <i>De Novo</i> Variant Caller for 16S rRNA Gene Data Sets
Farnaz Fouladi, Jacqueline B. Young, Anthony A. Fodor
Abstract
Recent bioinformatics development has enabled the detection of sequence variants with a high resolution of only one single-nucleotide difference in 16S rRNA gene sequence data. Despite this progress, there are several limitations that can be associated with variant calling pipelines, such as producing a large number of low-abundance sequence variants which need to be filtered out with arbitrary thresholds in downstream analyses or having a slow runtime.
Topics & Concepts
Sequence (biology)Computational biologyInferenceSmoothingBiologyScalabilityAlignment-free sequence analysisGeneticsComputer scienceSet (abstract data type)DNA sequencingGeneData miningFunction (biology)Sequence analysisRibosomal RNAGene predictionPipeline (software)Data set16S ribosomal RNASequence alignmentAlgorithmDeep sequencingGenomics and Phylogenetic StudiesGenomics and Rare DiseasesGenomic variations and chromosomal abnormalities