Fast and Sensitive Alignment of Microbial Whole Genome Sequencing Reads to Large Sequence Datasets on a Desktop PC: Application to Metagenomic Datasets and Pathogen Identification

Abstract

Next generation sequencing (NGS) of metagenomic samples is becoming a standard approach to detect individual species or pathogenic strains of microorganisms. Computer programs used in the NGS community have to balance between speed and sensitivity and as a result, species or strain level identification is often inaccurate and low abundance pathogens can sometimes be missed. We have developed Taxoner, an open source, taxon assignment pipeline that includes a fast aligner (e.g. Bowtie2) and a comprehensive DNA sequence database. We tested the program on simulated datasets as well as experimental data from Illumina, IonTorrent, and Roche 454 sequencing platforms. We found that Taxoner performs as well as, and often better than BLAST, but requires two orders of magnitude less running time meaning that it can be run on desktop or laptop computers. Taxoner is slower than the approaches that use small marker databases but is more sensitive due the comprehensive reference database. In addition, it can be easily tuned to specific applications using small tailored databases. When applied to metagenomic datasets, Taxoner can provide a functional summary of the genes mapped and can provide strain level identification. Taxoner is written in C for Linux operating systems. The code and documentation are available for research applications at http://code.google.com/p/taxoner.

Vectors of diversity: Genome wide diversity across the geographic range of the Chagas disease vector Triatoma dimidiata sensu lato (Hemiptera: Reduviidae)

“…This fasta file was then mapped, using Bowtie2 (Langmead and Salzberg, 2012) with default parameters, against all available Archaea, Bacteria, Fungi and Virus genomes, obtained using Taxoner (Pongor et al, 2014) and to the human genome. No contamination from these sources was observed.…”

Functional Changes in the Gut Microbiome Contribute to Transforming Growth Factor β-Deficient Colon Cancer

“…(B1) Flow chart showing number of reads at each step of DNA analysis. Reads were aligned to PATRIC ( 48 ) with Taxoner64 ( 95 ). The last step of the DNA analysis feeds into the second step of the RNA analysis.…”

“…Alignment was done with Taxoner64 version 0.1.3 ( 95 ) against the ~30,000 bacterial and archaeal genomes in PATRIC ( 48 ) (genomes downloaded on 5 September 2015 from https://www.patricbrc.org/ ) using the parameters “-A --very-sensitive-local” ( https://github.com/hurwitzlab/taxoner-patric ). Results were then filtered with a minimum alignment score of 131 (the average alignment score for H. hepaticus , our positive control) and a minimum count of ~138 (the average count of Mycoplasma pulmonis , a pathogen that is a negative control since the facility is specific pathogen free [SPF]).…”

In-Depth Resistome Analysis by Targeted Metagenomics

“…Reads were mapped against our database comprising ARG-ANNOT, BacMET and ConjDB databases independently, using Bowtie2 software 37 . Bowtie was set up to retrieve all end to end possible alignments and suppress both discordant alignments and mixed alignments.…”