Trim FASTA/Q files
Use trim_galore -- http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
Version 0.4.1
Requires cutadapt
trim_galore automatically detects gzip-compressed input files and strips that extension from the output file name
FASTA files are not processed correctly, and return an error from trim_galore.
Whether a files ends in fastq or fq, that extension will be stripped from the output file name
After stripping .gz and/or .fastq or .fq, the suffix _trimmed.fq will be appended to the name of the output file
By default, the output of trim_galore is gzip-compressed. Using the --dont_gzip flag ensures that the output is not compressed.
The second output file is a summary of the trimming that took place. That file has the name of the input file (retaining the .fastq/fq(.gz)) + _trimming_report.txt