#sam #bioinformatics #reader #writer #sequence #format

noodles-sam

Sequence Alignment/Map (SAM) format reader and writer

2 releases

0.1.1 Jul 21, 2021
0.1.0 Jul 14, 2021


Used in 7 crates (4 directly)

MIT license

355KB
7K SLoC

noodles

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, BGZF, CRAM 3.0, CSI, FASTA, FASTQ, GFF3, SAM 1.6, tabix, and VCF 4.3.

Usage

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 = "0.1.0", 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.bam

Related 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.

Dependencies

~1MB
~18K SLoC