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Acinetobacter Species Assignment Tool: XspecT


What is XspecT?

The 'Acinetobacter species Assignment Tool' (AspecT) will assign your given sequence-reads or assembled genome to a Acinetobacter species. If an assignment is not possible, it is not a species of Acinetobacter or not a species currently covered by the tool.

How it works

AspecT uses Bloom Filters to check k-mers from the input-data for exact matches with our database. It then taxonomically assigns the input-data to the Acinetobacter species with the k-mer most matches.
A Support Vector Machine (SVM) further ensures that closely related species, e.g. species of the A. calcoaceticus-A. baumannii-complex (ACB-complex), will be assigned correctly.

How to use the Tool

AspecT can take FASTA-files (.fq/.fna) as upload-data for assembled genomes and FASTQ-files (.fq) for sequence-reads. For sequence-reads you can choose the amount of reads that will be used for the assignment. 5000 reads are the minimum amount (with 100.000 Reads as maximum) sufficient for the toxonomic assignment. Using more reads can lead to a more accurate assignment but will take more time.

Please note that the tool was designed for high quality sequence-reads
(<1% Error-Rate) with a length of 125-250bp for each read (e.g. Illumina-Reads).
An accurate assignment using reads with a high error-rate is not guaranteed. Please also note that AspecT only requires a small amount of k-mers for the assignment so that not every k-mere from the assembled genome or sequence-read will be used. If you want to use all k-mers you can disable the quick-search. Beware of runtimes of about ~10 minutes.
Click here for more information on how AspecT performs the toxonomic assignment.
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