noodles
noodles is a library for handling various bioinformatics file formats. It currently includes readers and writers for BAM 1.6, BGZF, CRAM 3.0, FASTA, FASTQ, GFF3, SAM 1.6, tabix, and VCF 4.3.
Notably, the BAM and CRAM parsers are pure Rust implementations.
Usage
There is currently no release of noodles, as the API is still experimental, but it can be added to a test project as a preview.
noodles is split into multiple crates by file format. For convenience, a
top-level meta crate named noodles can be added to your project's dependency
list; and formats, listed as features. For example, to work with the BAM
format, enable the bam feature.
noodles = { git = "https://github.com/zaeleus/noodles.git", features = ["bam"] }Each enabled feature can then be imported by its re-exported name, e.g.,
use noodles::bam;Examples
Each crate may have its own examples directory, and all examples are runnable
as an application. After cloning the repository, run cargo run --release --example for a list of available examples. Use the example name as the option
argument and append program arguments to the command, e.g.,
cargo run --release --example bam_write > sample.bam
cargo run --release --example bam_read_header sample.bamRelated tools
noodles itself does not provide any applications, but related tools do depend on it.
- noodles-squab: Gene expression quantification by counting aligned record intersections on reference gene annotations.