noodles attempts to provide correct implementations of libraries for handling various bioinformatics file formats. It currently supports BAM 1.6, BCF 2.2, BED, BGZF, CRAM 3.0/3.1, CSI, FASTA, FASTQ, GFF3, GTF 2.2, SAM 1.6, tabix, and VCF 4.3/4.4.
noodles is published on [crates.io]. Early versions can be used in projects, but keep in mind that the API is still considered experimental.
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.
toml
noodles = { version = "0.41.0", features = ["bam"] }
Each enabled feature can then be imported by its re-exported name, e.g.,
rust
use noodles::bam;
Individual crates may have optional features that can be enabled using feature flags.
async: Enables asynchronous I/O with [Tokio]. (BAM, BCF, BGZF, CRAM, CSI,
FASTA, FASTQ, SAM, tabix, and VCF)libdeflate: Use [libdeflate] to encode and decode DEFLATE streams. (BGZF
and CRAM)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.,
bash
cargo run --release --example bam_write > sample.bam
cargo run --release --example bam_read_header sample.bam