- recipe trim-galore
Fast adapter and quality trimming for NGS data — Oxidized Edition (Rust)
- Homepage:
- Developer docs:
- License:
GPL / GPL-3.0-only
- Recipe:
- Links:
usegalaxy-eu: trim_galore
Trim Galore v2 is a Rust rewrite of the original Perl Trim Galore. Single static binary, no Python/Perl/Cutadapt/Java/igzip/pigz dependencies. Drop-in compatible with v0.6.x scripts and pipelines (same CLI, same output filenames, same report format) with adapter auto-detection (Illumina, Nextera, Small RNA, BGI/DNBSEQ), poly-G/poly-A trimming, paired-end single-pass processing, RRBS support, and bundled FastQC integration via fastqc-rust.
- package trim-galore¶
- Versions:
2.2.0-0,2.1.0-0,0.6.11-0,0.6.10-2,0.6.10-1,0.6.10-0,0.6.9-0,0.6.7-0,0.6.6-1,2.2.0-0,2.1.0-0,0.6.11-0,0.6.10-2,0.6.10-1,0.6.10-0,0.6.9-0,0.6.7-0,0.6.6-1,0.6.6-0,0.6.5-0,0.6.4-1,0.6.4-0,0.6.3-0,0.6.2-0,0.6.1-0,0.5.0-0,0.4.5-2,0.4.5-1,0.4.5-0,0.4.4-0,0.4.3-1,0.4.3-0,0.4.1-3,0.4.1-2,0.4.1-1,0.4.1-0- Additional platforms:
linux-aarch64,osx-arm64
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install trim-galore
to add into an existing workspace instead, run:
pixi add trim-galore
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install trim-galore
Alternatively, to install into a new environment, run:
conda create -n envname trim-galore
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/trim-galore:<tag>
(see trim-galore/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Notes¶
Linux x86_64, Linux aarch64, and macOS aarch64 (Apple Silicon) prebuilt binaries ship via the GitHub Releases page. Intel Mac users (osx-x86_64) should install via `cargo install trim-galore`, or pull the Docker linux/amd64 image (`docker pull ghcr.io/felixkrueger/trimgalore:latest` on Apple Silicon Docker also works — pulls the linux/arm64 multi-arch variant).
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/trim-galore/README.html)
