A Fast·a·q parser 🧬 💻

We have different fastx parser write in rust, this one was originaly create to be include in noodles but it's not fit in noodles crates target (it's ok he convinced me).

Usage

Add this in Cargo.toml dependency:

fastx = { git = "https://github.com/natir/fastx" }

No plans to add it to crates.io at this time.

Minimum supported Rust version

Currently the minimum supported Rust version is 1.56.0.

Evaluate parser

Criterion

Requirement:

• cargo criterion

cargo criterion

A html report is generate in ../target/criterion/reports/index.html

Hyperfine

Requirement:

• hyperfine
• seqtk
• a fastq file

Next script assume FASTQ variable contain path to fastq file.

cargo build --release --example fastq2fasta
hyperfine --warmup 3 -n fastx -n seqtk 'target/release/examples/fastq2fasta $FASTQ ' 'seqtk seq -A $FASTQ '