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Trim Galore!

Function	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
Language	Perl
Requirements	A functional version of Cutadapt and optionally FastQC are required.
Code Maturity	Stable.
Code Released	Yes, under GNU GPL v3 or later.
Initial Contact	Felix Krueger
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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 be run on the resulting output files once trimming has completed (optional)

Changelog

• 10-04-13: Version 0.2.8 released
• • Trim Galore will now compress output files with GZIP on the fly instead of compressing the trimmed file once trimming has completed. In the interest of time temporary files are not being compressed
  • Added a small sanity check to exit if no files were supplied for trimming. Thanks to P. for 'bringing this to my attention'
• 01-03-13: Version 0.2.7 released
• • Added a new option '--dont_gzip' that will force the output files not to be gzip compressed. This overrides both the '--gzip' option or a .gz line ending of the input file(s)
• 07-02-13: Version 0.2.6 released
• • Fixes some bugs which would not gzip or run FastQC correctly when the option '-o' had been specified
  • When '--fastqc' is specified in paired-end mode the intermediate files '_trimmed.fq' are no longer analysed (only files '_val_1' and '_val_2')
• 19-10-12: Version 0.2.5 released
• • Added option '-o/--output_directory' to redirect all output (including temporary files) to another folder (required for implementation into Galaxy)
  • Added option '--no_report_file' to suppress a report file
  • Added option '--suppress_warn' to suppress any output to STDOUT or STDERR
• 02-10-12: Version 0.2.4 released
• • Removed the shorthand '-l' from the description as it might conflict with the paired-end options '-r1/--length1' or '-r2/--length2'. Please use '--length' instead
  • Changed the reporting to show the true Phred score quality cutoff
  • Corrected a typo in stringency...
• 31-07-12: Version 0.2.3 released
• • Added an option '-e ERROR RATE' that allows one to specify the maximum error rate for trimming manually (the default is 0.1)
• 09-05-12: Version 0.2.2 released
• • Added an option '-a2/--adapter2' so that one can specify individual adapter sequences for the two reads of paired-end files; hereby the sequence provided as '-a/--adapter' is used to trim read 1, and the sequence provided as '-a2/--adapter2' is used to trim read 2. This option requires '--paired' to be specified as well
• 20-04-12: Version 0.2.1 released
• • Trim Galore! now has an option '--paired' which has the same functionality as the validate_paired_ends script we offered previously. This option discards read pairs if one (or both) reads of a read pair became shorter than a given 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
  • Paired-end reads may be truncated by a further 1 bp from their 3' end to avoid problems with invalid alignments with Bowtie 1 (which regards alignments that contain each other as invalid...)
  • The output may be gzip compressed (this happens automatically if the input files were gzipped (i.e. end in .gz))
  • The documentation was extended substantially. We also added some recommendations for RRBS libraries for MseI digested material (recognition motif TTAA)
• 21-03-12: Version 0.1.4 released
• • Phred33 (Sanger) encoding is now the default quality scheme
  • Fixed a bug for Phred64 encoding that would occur if several files were specified at once
• 14-03-12: Version 0.1.3 released
• • Initial stand-alone release; all basic functions working
  • Added the option 'fastqc_args' to pass extra options to FastQC

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