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Table 1 Example for tab-delimited table structure serving IMDA as input adapted from the barcode.txt file of the provided test data. The format is analog to the one used by MIGEC. This file should contain for each sample: a sample ID defining the name of the sample and the barcode sequence containing the barcode (here: CAGAT) and optional UMI (represented by “N”). Further, if available, an additional barcode sequence can be defined. Mandatory inputs are the FASTQ files containing all sequencing reads, forward (#1) and reverse (#2)

From: ImmunoDataAnalyzer: a bioinformatics pipeline for processing barcoded and UMI tagged immunological NGS data

#Sample ID Master barcode sequence (barcode and UMI) Additional barcode sequence FASTQ #1 FASTQ #2
1_A_nS_r1 NNNNNNtCAGATtNNNNNNtcttgggg   idx1_R1_001.fastq.gz idx1_R2_001.fastq.gz
1_A_nS_r2 NNNNNNtCAGATtNNNNNNtcttgggg   idx2_R1_001.fastq.gz idx2_R2_001.fastq.gz
2_A_nS_r1 ..   .. ..
2_A_nS_r2 .   . .