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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.

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.