Combined Phred quality Identification

1. Illumina PE read two fq Illumina PE read one fq Failed Filter Phred quality filtering Combined Phred quality Identification Phred quality Graph Discard read Filtering arguments Passed Filter Barcode Match quality and Identification Failed Filter Barcode quality filtering Barcode Match quality Graph Discard read Small database Barcode file Ribosomal database Large database Passed Filter Gzip compression of PE reads files Matched Barcode and Sequence in header Demultiplexed results in fasta Compressed Illumina PE read one file Compressed Illumina PE read two file Read one and read two sequences concatenation Barcode demultiplexing Manually curated USEARCH scan in small database Add to newly created database Not Found Found Read one and read two re-orientation No hits in small database USEARCH hits to fasta Full ribosomal sequence Create two orientations Join USEARCH results Local alignment of primer set in seq Concatenate extension sequences USEARCH scan in large database USEARCH hits to fasta Retrieval of alignment extension Retrieval of alignment extension

2. LEGEND SEQUENCING DATA DATABASE DECISION OUTPUT FILE USER ARGUMENTS DATA MERGE