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docker-trim-reads

Trim FASTA/Q files

Use trim_galore -- http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

Version 0.4.1

Requires cutadapt

File naming conventions

Gzip

trim_galore automatically detects gzip-compressed input files and strips that extension from the output file name

FASTA

FASTA files are not processed correctly, and return an error from trim_galore.

FASTQ/FQ

Whether a files ends in fastq or fq, that extension will be stripped from the output file name

_trimmed.fq

After stripping .gz and/or .fastq or .fq, the suffix _trimmed.fq will be appended to the name of the output file

Gzip output

By default, the output of trim_galore is gzip-compressed. Using the --dont_gzip flag ensures that the output is not compressed.

Trimming summary

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

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Trim FASTA/Q

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