What type of file can I use as input?

APECtyper only accepts assembly files (contigs or complete genome) in FASTA format. If you have FASTQ read files they will need to be assembled first.

Can I upload and run multiple assembly files at one time?

No, that is not possible with this version of APECtyper. Future versions may allow this.

What does it mean when the full pathotype says “Unknown High-Risk Status”?

Classifying a strain as high-risk depends on the input strain sequence type (ST) and O-antigen. If one or both of these pieces of information are missing, the high-risk classification may be reported as “Unknown”. For example, an ST155 isolate with an unknown O-antigen would have an “Unknown” high-risk classification because even though ST155 is not a high-risk ST, we cannot rule out O78 as the O-antigen. Alternatively, if the sequence type is known to be high-risk, such as ST131, a classification of "high-risk" would be reported regardless of whether the O-antigen is known.

Missing ST or O-antigen information could be due to quality control issues, such as contamination, low sequencing coverage, or poor de novo assembly. Additionally, if the ST profile is not included in the MLST scheme database, the ST would be reported as “-”. The ECTyper QC information may be helpful in identifying your specific issue.

Can I see all BLASTn hits, not just the ones with an identity ≥96% and query coverage per subject ≥90%?

No, not with the current version of APECtyper. The BLASTn thresholds used in APECtyper were determined based on analyses of a large number of poultry-source E. coli genomes. These thresholds reduce the likelihood of false positive hits due to poor alignment(s). That said, you can always download the APEC VF database from GitHub and run a nucleotide BLAST yourself.

Help! I still have questions. Who can I contact?

You can send an email to our team.