The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

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Sabre-barcode-demultiplexing

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Sabre will identify 5-prime terminal barcodes, sort the reads accordingly, and remove the barcode sequences and corresponding quality values.

Quick Start

Test Data

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Test data for this app appears directly in the Discovery Environment in the Data window under _Community Data -> iplantcollaborative -> example_data -> Sabre

Input File(s)

Use FFGLB5S04.fastq from the directory above as the example file for the FASTQ input.

Use barcodes.txt file as the example file for the barcodes field input.

Parameters Used in App

Choose single-ended or paired end reads. A barcode file is always needed.

For paired end reads, 2 separate forward and revers read files must be entered, and 2 paired output files for reads with no identified barcodes. The format for the barcode file is tab-delimited with 3 columns for paired end: barcode sequence, filename1, and filename2. 

  • For single reads, only one input sequence file is needed, and one output file for the unidentified reads. The barcode file is tab-delimited columns: barcode sequence and filename.
  • For both paired end and single reads, the maximum mismatch designates the maximum number of mismatches allowed in a barcode. The default is set to 0. A setting can be used to tell Sabre to expect barcodes on both forward and reverse reads in a pair.

Output File(s)

Expect a FASTQ file as output. For the test case, the output files you will find in the example_data directory are named sabreC_1.fq, sabreN_1.fq, and unknown1.fq.

Tool Source for App

For more information about Scythe and pre-processing sequences, please visit the Pre-processing Sequencing Reads on the iPlant Wiki in the Genome and Transcript Assembly space.

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