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NGSCheckMate
Verifies sample identities from FASTQ, BAM or VCF files. NGSCheckMate uses a model-based method to compare allele read fractions at known single-nucleotide polymorphisms (SNPs), considering depth-dependent behavior of similarity metrics for identical and unrelated samples. It is effective for a variety of data types, including exome sequencing, whole-genome sequencing, RNAseq, ChIP-seq, targeted sequencing and single-cell whole-genome sequencing, with a minimal requirement for sequencing depth. The tool can be used as a quality control step in next-generation sequencing (NGS) studies.
TEQC
Provides quality assessment of target enrichment experiments. TEQC enables users to leverage a multitude of methods to monitor the target enrichment process. Moreover, TEQC allows to evaluate the amount of read duplication and its effect on target coverage, as well as the relation between GC content of the capture hybridization probes and coverage for the respective bases. It imports genomic positions of sequencing reads and target regions, and allows to evaluate the whole enrichment process by estimating specificity and sensitivity of the capture, per-target read coverage and amount of read duplication.
BasePlayer
Enables tightly integrated comparative variant analysis and visualization of thousands of next generation sequencing (NGS) data samples and millions of variants. BasePlayer is a highly efficient and user-friendly software for biological discovery in large-scale NGS data. It transforms an ordinary desktop computer into a large-scale genomic research platform, enabling also a non-technical user to perform complex comparative variant analyses, population frequency filtering and genome level annotations under intuitive, scalable and highly-responsive user interface to facilitate everyday genetic research as well as the search of novel discoveries.
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