NGSCheckMate

NGSCheckMate is a user-friendly software package that provides a standardized metric for genotype comparisons to verify sample identities from FASTQ, BAM or VCF files in next-generation sequencing (NGS) studies. It uses a model-based method to compare allele read fractions at known single-nucleotide polymorphisms, considering the depth-dependent behavior of similarity metrics for identical and unrelated samples. It is effective for a variety of data types, with a minimal requirement for sequencing depth, and includes an alignment-free module for a quick initial check. It is recommended as a quality control step for NGS studies.

Topic

NGS;Whole genome sequencing;RNA-seq;Data quality management

Detail

  • Operation: Sequencing quality control

  • Software interface: Command-line user interface

  • Language: R;Python

  • License: The MIT licence

  • Cost: Free

  • Version name: ncm-1.0.0

  • Credit: Harvard Medical School Eleanor and Miles Shore Fellowship, Randolph Hearst Fund, National Institute on Aging, National Institute of Mental Health, National Eye Institute, Korean Health Technology Project, Ministry of Health, Welfare, Republic of Korea, National Institutes of Health (NIH).

  • Input: bam, .vcf, FASTQ

  • Output: Text, PDF

  • Contact: peter_park@hms.harvard.edu

  • Collection: -

  • Maturity: -

Publications

  • NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types.
  • Lee S, et al. NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types. NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types. 2017; 45:e103. doi: 10.1093/nar/gkx193
  • https://doi.org/10.1093/nar/gkx193
  • PMID: 28369524
  • PMC: PMC5499645

Download and documentation

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