Search Results for "snv"
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Showing 12 open source projects for "snv"
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MetaEntropy
R package for Virome Mutational Analysis
...Provides normalized values (0-1 scale) to facilitate the direct comparison of different genomic positions or total functional entropy across multiple metagenomes. Designed to analyze mutational data using tabular 'Single Nucleotide Variant' (SNV) frequency tables generated by variant callers (e.g., 'iVar' or 'LoFreq'), operating independently of consensus sequence estimation and multiple sequence alignment. -
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RePlow
Replicate-based caller for the accurate detection of low-frequency SNV
...RePlow accurately detects such low-level mutations based on the probabilistic model that jointly analyzes library-level replicates, regardless of the sequencing platform. The important features of RePlow are: • On-the-fly 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 -
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Nuvarator
A SNV Detection Software Tools Installer Package
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 to researchers interested in evolutionary biology, and hence lays the foundation for predicting disease susceptibility and drug response. ... -
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karkinos
Tumor genotyper for Exome sequence that detects SNV,CNV, aTumor purity
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. -
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MNV Annotation Corrector
Multi-nucleotide Variation Annotation Corrector for NGS SNV callers
...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 of user-provided SNVs and the matching BAM file to accurately identify MNV, and use existing annotators (currently supports ANNOVAR/SnpEff/VEP) to provide corrected amino acid prediction. -
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MethylExtract
High-Quality methylation maps and SNV calling from BS-Seq experiments
MethylExtract is a user friendly tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation. The program is implemented into a single script and takes into account all major error sources: sequencing errors, bisulfite failure, clonal reads and single nucleotide variants. MethylExtract detects variation (SNVs – Single Nucleotide Variation) in a similar way than VarScan, a very sensitive method extensively used in... -
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MERAP
Medical Resequencing Analysis Pipeline
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PlaTypUS
Plasmodium Typing Utility Software
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. -
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QuasiRecomb
Probabilistic inference of viral Quasispecies
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... -
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