ENAapplication/xmlftp.sra.ebi.ac.uk/vol1/fastq/ERR179/001/ERR1797921/ERR1797921.fastq.gzftp.sra.ebi.ac.uk/vol1/fastq/ERR179/007/ERR1797917/ERR1797917.fastq.gzftp.sra.ebi.ac.uk/vol1/fastq/ERR179/005/ERR1797915/ERR1797915.fastq.gzftp.sra.ebi.ac.uk/vol1/fastq/ERR179/003/ERR1797923/ERR1797923.fastq.gzftp.sra.ebi.ac.uk/vol1/fastq/ERR179/009/ERR1797919/ERR1797919.fastq.gzftp.sra.ebi.ac.uk/vol1/fastq/ERR179/004/ERR1797924/ERR1797924.fastq.gzftp.sra.ebi.ac.uk/vol1/fastq/ERR179/003/ERR1797913/ERR1797913.fastq.gzftp.sra.ebi.ac.uk/vol1/fastq/ERR179/002/ERR1797922/ERR1797922.fastq.gzftp.sra.ebi.ac.uk/vol1/fastq/ERR179/008/ERR1797918/ERR1797918.fastq.gzftp.sra.ebi.ac.uk/vol1/fastq/ERR179/006/ERR1797916/ERR1797916.fastq.gzftp.sra.ebi.ac.uk/vol1/fastq/ERR179/001/ERR1797911/ERR1797911.fastq.gzftp.sra.ebi.ac.uk/vol1/fastq/ERR179/004/ERR1797914/ERR1797914.fastq.gzftp.sra.ebi.ac.uk/vol1/fastq/ERR179/002/ERR1797912/ERR1797912.fastq.gzftp.sra.ebi.ac.uk/vol1/fastq/ERR179/000/ERR1797920/ERR1797920.fastq.gzprimaryOK2000000GenomicsUCSDMIhttps://www.ebi.ac.uk/ena/browser/view/PRJEB19022High-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 - DS92017-01-172017-01-17PRJEB19022232024351154581