Search Results for "snv"

... estimation of the VAF distribution of background errors • Improved low-level SNV calling based on the estimated error profiles and the observation concordance between replicates

A software package Nuvarator which downloads and installs different tools related to Somatic SNV detection. SNV detection is range of computational tech- niques and algorithms used to identify the existence of single nu- cleotide variants (SNVs) by using the result from Next Generation Sequencing (NGS) experiments. NGS are methods employed for Whole Genome Sequencing, a process for determining the precise order of nucleotides within a DNA molecule which can improve the knowledge available...

karkinos is tumor genotyper which detects single nucleotide variation (SNV), integer copy number variation (CNV) and calculates tumor cellularity from tumor-normal paired sequencing data. Accurate CNV calling is achieved using continuous wavelet analysis and multi-state HMM, while SNV call is adjusted by tumor cellularity and filtered by heuristic filtering algorithm and Fisher Test. Also, Noise calls in low depth region are removed using EM algorithm.

MAC is an Ad hoc software designated to fix incorrect amino acid predictions caused by multiple nucleotide variations (MNVs). These complex mutations consist of two or more consecutive nucleotide substitutions, but can only be detected in the format of several single nucleotide variations (SNV) by most variant callers and annotated separately, which likely leads to incorrect amino acid prediction when more than one mutated bases occur within the same protein codon. MAC screens through a list...

The goal of PlaTypUS is to establish a unified Plasmodium whole genome analysis tool, that aligns short read sequences in an agreed upon manner, with many quality control steps, and calls both SNVs and CNVs in a community agreed standard way. We also seek to provide this analysis in a stand-alone graphic user interface so that labs around the world can analyze their own whole genome sequencing data, rather than relying on outside institutes.

Please get the binary latest version at https://github.com/armintoepfer/QuasiRecomb/releases Description: RNA viruses are present in a single host as a population of different but related strains. This population, shaped by the combination of genetic change and selection, is called quasispecies. Genetic change is due to both point mutations and recombination events. We present a jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its...