PaSD-qc

PaSD-qc (Power Spectral Density-qc) is a tool for analyzing the properties and quality of single-cell whole-genome sequencing (scWGS) data. The PaSD-qc algorithm uses power spectral density estimation to estimate amplification uniformity and size distribution, autocovariance and inter-sample consistency, and aberrant read-density profiles.

Topic

Genomics;Sequencing;Quality affairs

Detail

  • Operation: Sequencing quality control

  • Software interface: Library

  • Language: Python

  • License: The MIT License

  • Cost: Free

  • Version name: 1.1.3

  • Credit: National Institutes of Health, National Institute of Neurological Disorders and Stroke, National Institute on Aging, Harvard Ludwig Center, the Howard Hughes Medical Institute.

  • Input: -

  • Output: -

  • Contact: Maxwell A Sherman maxwell_sherman@hms.harvard.edu, Peter J Parkpeter_park@hms.harvard.edu

  • Collection: -

  • Maturity: -

Publications

  • PaSD-qc: quality control for single cell whole-genome sequencing data using power spectral density estimation.
  • Sherman MA, Barton AR, Lodato MA, Vitzthum C, Coulter ME, Walsh CA, Park PJ. PaSD-qc: quality control for single cell whole-genome sequencing data using power spectral density estimation. Nucleic Acids Res. 2018 Feb 28;46(4):e20. doi: 10.1093/nar/gkx1195. PMID: 29186545; PMCID: PMC5829578.
  • https://doi.org/10.1093/nar/gkx1195
  • PMID: 29186545
  • PMC: PMC5829578

Download and documentation

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