Bug#933975: ITP: trim-galore -- automate quality and adapter trimming for DNA sequencing
Package: wnpp
Severity: wishlist
Subject: ITP: trim-galore -- automate quality and adapter trimming for DNA sequencing
Package: wnpp
Owner: Steffen Moeller <moeller@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
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