Quality-, adapter- and RRBS-trimming with Trim Galore!

[fkrueger]

I am glad that you found it useful!

[gwilkie]

Thanks so much for writing this incredibly useful program

I was struggling with the problem of trimming and removing low quality reads whilst maintaining read pairs - trim galore makes this straightforward and fast!

[fkrueger]

We have just updated Trim Galore! so that is now has built-in paired-end functionality which means that trimmed files don't need to be validated separately any more, as well as a few more things that make it more convenient to use.

As there hasn't been any dedicated thread yet, here are a few more details: Trim Galore! is a wrapper script to automate quality and adapter trimming, with some added functionality to remove biased methylation positions for MspI digested 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 be run on the resulting output files once trimming has completed (optional)

Trim Galore! and its User Guide can be found here: http://www.bioinformatics.babraham.a...s/trim_galore/