Package: trim-galore (0.6.5-1)

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