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Format Fastq sequences and barcode data (version
This file is considered read 1
This applies to the –fastq1 file and all options specified by –input_type
NOTE: Must contain a header line indicating SampleID in the first column and BarcodeSequence in the second, LinkerPrimerSequence in the third and a ReversePrimer column before the final Description column. Needed for –attempt_read_orientation option.
An exact match for the forward and reverse complemented versions of the primers are tested for, and sequences are reverse complemented, if necessary, before writing. Sequences without an exact match are written to a separate output fastq file, labeled as _no_primer_match.fastq.

What it does

This script is designed to format fastq sequence and barcode data so they are compatible with

A variety of data formats are possible, depending upon how one utilized sequencing primers, designed primer constructs (e.g., partial barcodes on each end of the read), or processed the data (e.g., barcodes were put into the sequence labels rather than the reads). See various input examples below.

More information about this tool is available on QIIME documentation.