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:
Trim Galore is now also available from GitHub. You are invited to leave comments, feature request or bug reports over there!

•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)



FastQC Options

Folder for output files
Create all output files in the specified output directory. Please note that this directory must exist as the program will not create it. If this option is not set then the output file for each sequence file is created in the same directory as the sequence file which was processed.
Number of threads
Specifies the number of files which can be processed simultaneously. Each thread will be allocated 250MB of memory so you shouldn't run more threads than your available memory will cope with, and not more than 6 threads on a 32 bit machine
Additional FastQC options.
For all additional FastQC options not offered above. Please consult the official FastQC documentation for assistance in configuring these options."

Preference page

Set a threshold for repeated execution. Only used if HTE is enabled in the preference page.

Input Ports

Cell 0: Path to ReadFile1
Cell 1 (Optional): Path to ReadFile2.

Output Ports

Cell 0: Path to TrimmedReadFile1
Cell 1 (Optional): Path to TrimmedReadFile2.

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