trimgalore

Latest release

The latest release is v0.4.5.1. Be warned, that trimgalore itself will report v0.4.4_dev, but that is an error in the trimgalore release and already reported.

Docker images

Based on last Release (v0.4.5.1):

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Latest image:

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Based on master branch:

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Based on develop branch:

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Usage:

Due to the image has trimgalore as entry point, calling docker run will return the help text:

$ docker run --rm -it imetools/trimgalore:v0.4.5
###
###    USAGE:
###
###   trim_galore [options] <filename(s)>
###
###
###   -h/--help               Print this help message and exits.
###
###   -v/--version            Print the version information and exits.
###
###   -q/--quality <INT>      Trim low-quality ends from reads in addition to adapter removal. For
###                           RRBS samples, quality trimming will be performed first, and adapter
###                           trimming is carried in a second round. Other files are quality and adapter
###                           trimmed in a single pass. The algorithm is the same as the one used by BWA
###                           (Subtract INT from all qualities; compute partial sums from all indices
###                           to the end of the sequence; cut sequence at the index at which the sum is
###                           minimal). Default Phred score: 20.
###
###   --phred33               Instructs Cutadapt to use ASCII+33 quality scores as Phred scores
###                           (Sanger/Illumina 1.9+ encoding) for quality trimming. Default: ON.
[...]

The version of trimgalore is returned, if --version is used as command:

$ docker run --rm -it imetools/trimgalore:v0.4.5 --version
###
###                             Quality-/Adapter-/RRBS-Trimming
###                                  (powered by Cutadapt)
###                                     version 0.4.4_dev
###
###                                Last update: 24 03 2017
###

Therefore you can almost use trimgalore like a local installation.

License

This repo is licences under MIT licence. For further information please check the content of the (LICENSE) file.

Issues

If you have any issues concerning the image or the repository, please report them via issues.

Author

This repository is created and maintained by Frank Förster.

Changelog

• v0.4.5.1 Adding parallel and new FastQC to image
  • trimgalore v0.4.5 (selfreporting as v0.4.4_dev)
  • FastQC v0.11.7
  • GNU parallel 20141022
• v0.4.5 First official release of the image. It includes
  • trimgalore v0.4.5 (selfreporting as v0.4.4_dev)
  • FastQC v0.11.4