Fast and safe Q/C for FASTQ files.
FastqScan is a command line (CLI) application for performing quality control of FASTQ files.
The application takes either a single FASTQ file for (single-end) sequencing or two (paired-end) FASTQ files, and reports the following Q/C metrics:
- average base quality (Phred)
- average quality of all reads
- average proportions of
{A, C, G, T, N}for each read position - average G/C content per read position
- average G/C content per read
- distribution of lengths of the individual reads
The metrics are reported to STDOUT in a JSON format.
Summarize single-end sequencing:
cargo run -- -1 data/example.R1.fastq.gzSummarize paired-end sequencing:
cargo run -- -1 data/example.R1.fastq.gz -2 data/example.R2.fastq.gz