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A bioconductor package for sample quality check with next generation sequencing data

Bioconductor version: Release (3.19)

The SeqSQC is designed to identify problematic samples in NGS data, including samples with gender mismatch, contamination, cryptic relatedness, and population outlier.

Author: Qian Liu [aut, cre]

Maintainer: Qian Liu <qliu7 at>

Citation (from within R, enter citation("SeqSQC")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Sample Quality Check for Next-Generation Sequencing Data with SeqSQC HTML R Script
Reference Manual PDF


biocViews Experiment Data, Genome, Homo_sapiens_Data, Project1000genomes, Sequencing Data, Software
Version 1.26.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL-3
Depends R (>= 3.4), ExperimentHub(>= 1.3.7), SNPRelate(>= 1.10.2)
Imports e1071, GenomicRanges, gdsfmt, ggplot2, GGally, IRanges, methods, plotly, RColorBrewer, reshape2, rmarkdown, S4Vectors, stats, utils
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Follow Installation instructions to use this package in your R session.

Source Package SeqSQC_1.26.0.tar.gz
Windows Binary
macOS Binary (x86_64) SeqSQC_1.26.0.tgz
macOS Binary (arm64) SeqSQC_1.26.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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