#gff #bioinformatics #reader #writer


Generic Feature Format (GFF) reader and writer

9 releases (breaking)

Uses new Rust 2021

0.7.0 Aug 16, 2022
0.6.1 Jun 8, 2022
0.6.0 Mar 29, 2022
0.5.0 Feb 17, 2022
0.1.1 Jul 21, 2021
Download history 65/week @ 2022-06-09 15/week @ 2022-06-16 28/week @ 2022-06-23 40/week @ 2022-06-30 87/week @ 2022-07-07 64/week @ 2022-07-14 100/week @ 2022-07-21 21/week @ 2022-07-28 50/week @ 2022-08-04 57/week @ 2022-08-11 51/week @ 2022-08-18 37/week @ 2022-08-25 49/week @ 2022-09-01 143/week @ 2022-09-08 131/week @ 2022-09-15 139/week @ 2022-09-22

468 downloads per month
Used in 3 crates (2 directly)

MIT license



crates.io Docs.rs CI status

noodles is a library for handling various bioinformatics file formats. It currently includes readers and writers for BAM 1.6, BCF 2.2, BED, BGZF, CRAM 3.0, CSI, FASTA, FASTQ, GFF3, GTF 2.2, SAM 1.6, tabix, and VCF 4.3.


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.

noodles = { version = "0.26.0", features = ["bam"] }

Each enabled feature can then be imported by its re-exported name, e.g.,

use noodles::bam;

Feature flags

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)


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.bam