SeqGuard is a Rust-based program for FASTQ checking, mainly for Phred+33 FASTQ. It checks for:

1. FASTQ 4-line format or empty file
2. Invalid nucleotide (non-ATGC character)
3. Invalid QV character (ASCII <0 or > 93)
4. Mismatch length of sequence and QV
5. Duplicate headers

Download a ready-to-use binary from the release page.

You may have to change the file permissions with chmod +x seqgurad;

Only -i or --input is needed, output to standard output

FASTQ quality check, based on Rust

Usage: seqguard [OPTIONS] --input <INPUT>

Options:
  -i, --input <INPUT>      Path to .fastq or .fastq.gz file
  -h, --help               Print help
  -V, --version            Print version

seqgurad -i test.fastq;
seqgurad -i test.fastq > result.txt;

Small FASTQ files are provided (here)[./tests]. You can use it as input for testing.

For a 40G FASTQ file, memory peak at ~2G, finished in ~1 minute.

The actual performance may vary depending on factors such as I/O speed, memory speed, and CPU capabilities.

Developed on rustc 1.77.2 (25ef9e3d8 2024-04-09), tested on single AMD EPYC 7K62, 256G of DDR4 2400 RAM, and SATA SSD storage.