and indicate forward and reverse reads, respectively.
The reverse reads were processed with a BWA style trimming script to remove low quality sequences.
Ribosomal reads were removed by aligning the reverse reads to ribosomal sequences using STAR26.
The forward and reverse reads were joined with no mismatches permitted.
Both forward and reverse reads as well as joined paired ends were compared against the databases using DIAMOND v0.5.321.
Forward and reverse reads were joined using the fast-join method and the resulting.fastq file was used to generate quality (.qual) and reads (.fasta) files for further processing.
Prepared libraries were subjected to paired-end sequencing on a SOLiD 5500 platform (Life Technologies, Carlsbad, CA, USA) with 75 bases forward reads and 35 bases reverse reads.
Fragments were included in further analyses if their forward and reverse reads overlapped by at least 11 base pairs (bp) and thus could be merged into single sequences.
The program sort_read_pairs.pl in STACKS was used to collect the reverse reads (the read pairs) of the outlier loci, and of 1,000 random loci of the catalog in order to construct a reference set for further enrichment analyses.
Then the treated forward and reverse reads were merged with PANDAseq (Masella et al. 2012).
The forward and reverse reads were joined and assigned to samples based on barcodes, and truncated by cutting off the barcode and primer sequences.
