Package: wnpp Severity: wishlist Subject: ITP: trim-galore -- automate quality and adapter trimming for DNA sequencing Package: wnpp Owner: Steffen Moeller <moel...@debian.org> Severity: wishlist
* Package name : trim-galore Version : 0.6.4 Upstream Author : Felix Krueger * URL : https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ * License : GPL-3.0+ Programming Lang: (C, C++, C#, Perl, Python, etc.) 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 Remark: This package is maintained by Steffen Moeller at https://salsa.debian.org/med-team/trim-galore
