Lake sediment Metagenome. freshwater sediment metagenome

As new sequencing technologies become cheaper and old ones disappear, laboratories must switch vendors and platforms. Validating the new setups is a crucial part in conducting rigorous scientific research. Here we report on the reliability and biases of performing bacterial 16S rRNA gene amplicon paired-end sequencing on the MiSeq Illumina platform. We designed a protocol using 50 barcode pairs to run samples in parallel and coded a pipeline to process the data. Sequencing the same sediment sample in 248 replicates, we evaluated the performance of the method with regards to estimates of alpha and beta diversity.