Results for "number"
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PureCN: copy number calling and SNV classification using targeted short read sequencing
This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number...Tags: PureCN, copy, number, calling, SNV, classification, targeted, short, read, sequencing
2100 days ago
EXCAVATOR: detecting copy number variants from whole-exome sequencing data
EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies genomic regions into five copy number states. We vali...Tags: EXCAVATOR, detect, copy, number, variants, whole-exome, sequencing, data
1951 days ago
ClinCNV: Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
ClinCNV detects CNVs in germline and somatic context in NGS data (targeted and whole-genome). We work in cohorts, so it makes sense to try ClinCNV if you have more than 10 samples (recommended amount - 40 since we estimate variances from the data). By "cohort" we mean samples sequenced ...Tags: ClinCNV, Detection, copy, number, changes, Germline, Trio, Somatic, NGS, data
1574 days ago
HairSplitter: assembling long reads in an unknown number of haplotypes
Pros and cons of HairSplitter Limitations of HairSplitter: Not very fast: it re-polishes the whole assembly Limited in the number of haplotypes Strengths of HairSplitter: Very modular, can be used with any assembler Naive: makes no assumption on ploidy, parameter-free Safe: won’...Tags: HairSplitter, assembling, long, reads, unknown, number, haplotypes
519 days ago
