Ultra-fast summary for fastx files
This is a stripped-down version of my other Rust program, faster, with less functionality but focused on speed. It is arguably the fastest tool that gives summary information about fastq files. The program uses the kseq library for reading fastx files and outputs various summary metrics.
A linux executable can be downloaded from the release section. Compiling for other platforms see below.
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
git clone https://github.com/angelovangel/faster2.git
cd faster2
cargo build --release
# the binary is now under ./target/release/, run it like this:
./target/release/faster2 -t /path/to/fastq/file.fastq.gz# simple
faster2 -t file.fastq
# the query file can be fasta, fastq, fastq.gz...The benchmarks were performed with sampled Nanopore (Zymo mock community dataset) data using hyperfine. faster2 was compared to faster, seqkit stats and seqstats.
