TY  - JOUR
U1  - Zeitschriftenartikel, wissenschaftlich - begutachtet (reviewed)
A1  - Davenport, Colin F.
A1  - Neugebauer, Jens
A1  - Beckmann, Nils
A1  - Friedrich, Benedikt
A1  - Kameri, Burim
A1  - Kokott, Svea
A1  - Paetow, Malte
A1  - Siekmann, Björn
A1  - Wieding-Drewes, Matthias
A1  - Wienhöfer, Markus
A1  - Wolf, Stefan
A1  - Tümmler, Burkhard
A1  - Ahlers, Volker
A1  - Sprengel, Frauke
T1  - Genometa - A Fast and Accurate Classifier for Short Metagenomic Shotgun Reads
JF  - PLOS One
N2  - Metagenomic studies use high-throughput sequence data to investigate microbial communities in situ. However, considerable challenges remain in the analysis of these data, particularly with regard to speed and reliable analysis of microbial species as opposed to higher level taxa such as phyla. We here present Genometa, a computationally undemanding graphical user interface program that enables identification of bacterial species and gene content from datasets generated by inexpensive high-throughput short read sequencing technologies. Our approach was first verified on two simulated metagenomic short read datasets, detecting 100% and 94% of the bacterial species included with few false positives or false negatives. Subsequent comparative benchmarking analysis against three popular metagenomic algorithms on an Illumina human gut dataset revealed Genometa to attribute the most reads to bacteria at species level (i.e. including all strains of that species) and demonstrate similar or better accuracy than the other programs. Lastly, speed was demonstrated to be many times that of BLAST due to the use of modern short read aligners. Our method is highly accurate if bacteria in the sample are represented by genomes in the reference sequence but cannot find species absent from the reference. This method is one of the most user-friendly and resource efficient approaches and is thus feasible for rapidly analysing millions of short reads on a personal computer.
KW  - BLAST algorithm
KW  - Metagenomics
KW  - Sequence alignment
KW  - Genomic databases
KW  - Bacterial genomics
Y1  - 2012
UN  - https://nbn-resolving.org/urn:nbn:de:bsz:960-opus4-8509
U6  - https://doi.org/10.25968/opus-850
DO  - https://doi.org/10.25968/opus-850
VL  - 7
IS  - 8
SP  - 8
S1  - 8
ER  -