Source: trim-galore Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller Section: science Priority: optional Build-Depends: debhelper-compat (= 13) Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/trim-galore Vcs-Git: https://salsa.debian.org/med-team/trim-galore.git Homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Rules-Requires-Root: no Package: trim-galore Architecture: all Depends: ${misc:Depends}, ${perl:Depends}, cutadapt Recommends: fastqc Description: automate quality and adapter trimming for DNA sequencing Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). It's main features are: * For adapter trimming, Trim Galore! uses the first 13 bp of Illumina standard adapters ('AGATCGGAAGAGC') by default (suitable for both ends of paired-end libraries), but accepts other adapter sequence, too * For MspI-digested RRBS libraries, Trim Galore! performs quality and adapter trimming in two subsequent steps. This allows it to remove 2 additional bases that contain a cytosine which was artificially introduced in the end-repair step during the library preparation * For any kind of FastQ file other than MspI-digested RRBS, Trim Galore! can perform single-pass adapter- and quality trimming * The Phred quality of basecalls and the stringency for adapter removal can be specified individually * Trim Galore! can remove sequences if they become too short during the trimming process. For paired-end files Trim Galore! removes entire sequence pairs if one (or both) of the two reads became shorter than the set length cutoff. Reads of a read-pair that are longer than a given threshold but for which the partner read has become too short can optionally be written out to single-end files. This ensures that the information of a read pair is not lost entirely if only one read is of good quality * Trim Galore! can trim paired-end files by 1 additional bp from the 3' end of all reads to avoid problems with invalid alignments with Bowtie 1 * Trim Galore! accepts and produces standard or gzip compressed FastQ files * FastQC can optionally be run on the resulting output files once trimming has completed