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SeqQC

SeqQC is an R package for basic quality control of DNA sequences in FASTA files.
It provides functions to import FASTA data and compute common QC metrics such as GC%, N-content, and sequence validity, and generate a QC report.

Features

  • FASTA import
  • GC% calculation
  • N-content calculation
  • Sequence validity checks
  • QC report with pass/fail flags and reasons
  • Unit tests using testthat

Installation

# install.packages("remotes")
remotes::install_github("PredVI/SeqQC")

Usage

library(SeqQC)

seqs <- read_fasta("example.fasta")
seq_qc(seqs)
qc_report(seqs)

License

MIT

Citation

If you use SeqQC in your work, please cite:

Elsharkawy, M. T. (2026). SeqQC: FASTA Sequence Quality Control Package (R). Zenodo. https://doi.org/10.5281/zenodo.18369549

Author

Mohammad Elsharkawy