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FelixKrueger / TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
GNU General Public License v3.0
467 stars 151 forks source link

Run TrimGalore on a FASTA input #139

Closed vkkodali closed 2 years ago

vkkodali commented 2 years ago

Is there a way to run TrimGalore on FASTA input files? I am only in interested in automatic detection of the adapters and trimming them without quality trimming.

FelixKrueger commented 2 years ago

Trim Galore doesn't explicitely handle FastA format, but there is a chance that it will work nevertheless as I think Cutadapt (which does the trimming itself) should auto-detect the file format. Otherwise there are numerous options online to convert FastA to FastQ very quickly.

If you don't want to perform quality trimming you can just set -q 0, which should only trim adapter sequences. I hope this helps.