Laelatu dataset containing two Illumina MiSeq runs

Laelatu testset contains 36 samples and two Illumina MiSeq runs: (i) arbuscular mycorrhizal fungal (AMF) reads and (ii) general eukaryote (F574) + general fungal ITS (ITS) reads. For each set sample sheets are provided in files AMF.txt, F574.txt and ITS.txt. Sample sheets are tab-delimeted, where columns from 1st to 5th are following: sample name, forward barcode sequence, forward primer sequence, reverse barcode sequence and reverse primer sequence.<br>AMF.txt sample sheet file has to be used with following FASTQ files: AMF_R1.fq.gz (forward reads containing forward primer and sequence), AMF_R2.fq.gz (forward reads containing barcode), AMF_R3.fq.gz (reverse reads containing barcode) and AMF_R4.fq.gz (reverse reads containing reverse primer and sequence).<br>F574.txt and ITS.txt sample sheet files have to be used with following FASTQ files: F574+ITS.R1.fq.gz (forward reads containing forward primer and sequence), F574+ITS.I1.fq.gz (forward reads containing barcode), F574+ITS.I2.fq.gz (reverse reads containing barcode) and F574+ITS.R2.fq.gz (reverse reads containing primer and sequence).<br>gDAT (github.com/ut-planteco/gDAT) pipeline supports usage of packed files (*.gz). Follow pipeline manual located in the manual/ folder how to proceed with the data analyses.