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Format Fastq sequences and barcode data (version 1.9.1.0)

Input fastq filepath:

This file is considered read 1

Reverse complement barcode 1 before writing?:

Length, in base pairs, of barcode 1:

This applies to the –fastq1 file and all options specified by –input_type

Input type:

Mapping files:

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.

Attempt to search for the forward and reverse primer in the read and adjust the sequence orientation to match the orientation of the forward primer?:

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.

Suppress header matching between input fastq files?:

What it does

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

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.