ITSxpress: software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis

Authors: Rivers, Adam; Weber, Kyle; GARDNER, TERRENCE - North Carolina State University; LIU, SHUANG - North Carolina State University; ARMSTRONG, SHALAMAR - Purdue University

Submitted to: F1000Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/24/2018
Publication Date: 9/6/2018
Citation: Rivers, A.R., Weber, K.C., Gardner, T.G., Liu, S., Armstrong, S. 2018. ITSxpress: software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis. F1000Research. 7:1418. https://doi.org/10.12688/f1000research.15704.1.
DOI: https://doi.org/10.12688/f1000research.15704.1

Interpretive Summary: Fungi play important roles in soil, plant and animal health. It is now possible to sequence a portion of the DNA from most fungi in a particular sample of soil or plant material. This sequenced portion of DNA serves as a fingerprint for each kind of fungus. The software developed here, ITSxpress, enables scientists to select just the most informative part of the fingerprint so they can better identify different kinds of fungi in a sample and their relative abundances. ITSxpress is 14-23 times faster than existing methods, enables scientists to use a more accurate method for identifying fungi and has a user interface that ties into popular existing software for identifying fungi.

Technical Abstract: The internally transcribed spacer (ITS) region between the small subunit ribosomal RNA gene and large subunit ribosomal rRNA gene is a widely used phylogenetic marker for fungi and other taxa. The eukaryotic ITS contains the conserved 5.8s rRNA and is divided into the ITS1 and ITS2 hypervariable regions. These regions are variable in length and are amplified using primers complementary to the conserved regions of their flanking genes. Previous work has shown that removing the conserved regions results in more accurate taxonomic classification. An existing software program, ITSx, is capable of trimming FASTA sequences by matching hidden Markov model profiles to the ends of the conserved genes using the software suite Hmmer. ITSxpress was developed to extend this technique from marker gene studies using Operational Taxonomic Units (OTU’s) to studies using exact sequence variants; a method used by the software packages Dada2, Deblur, Qiime2 and Unoise. The sequence variant approach uses the quality scores of each read to identify sequences that are statistically likely to represent real sequences. ITSxpress enables this by processing FASTQ rather than FASTA files. The software also speeds up the trimming of reads by a factor of 14-23x on a typical 4 core computer by temporarily clustering highly similar sequences that are common in amplicon data and utilizing optimized parameters for Hmmsearch. ITSxpress is available as a Qiime2 plugin and a stand-alone application installable from the Python package index, Bioconda and Github.