ENAapplication/xmlftp.sra.ebi.ac.uk/vol1/fastq/ERR178/001/ERR1780471/ERR1780471.fastq.gzftp.sra.ebi.ac.uk/vol1/fastq/ERR178/002/ERR1780472/ERR1780472.fastq.gzftp.sra.ebi.ac.uk/vol1/fastq/ERR178/004/ERR1780474/ERR1780474.fastq.gzftp.sra.ebi.ac.uk/vol1/fastq/ERR178/003/ERR1780473/ERR1780473.fastq.gzprimaryOK2000000GenomicsUCSDMIhttps://www.ebi.ac.uk/ena/browser/view/PRJEB18918High-throughput sequencing has revolutionized microbial ecology, but read quality remains a considerable barrier to accurate taxonomy assignment and alpha-diversity assessment for microbial communities. We demonstrate that high-quality read length and abundance are the primary factors differentiating correct from erroneous reads produced by Illumina GAIIx, HiSeq and MiSeq instruments. We present guidelines for user-defined quality-filtering strategies, enabling efficient extraction of high-quality data and facilitating interpretation of Illumina sequencing results.ENA0.00.00.00.00.00falseQuality-filtering vastly improves diversity estimates from Illumina amplicon sequencing - DS22017-01-102017-01-12PRJEB18918232024351306859