Why choose StrainSeeker for bacterial identification?

StrainSeeker's strengths

StrainSeeker's limitations

Testing StrainSeeker on metagenomic samples

Sample 1 - large simulated metagenome consisting of more than 800 bacteria and archae

This sample was used in a study that compared 14 of the existing metagenome analysis tools View publication

StrainSeeker results | Samples (we used Set_A1 and Set_B1) | Community composition table

StrainSeeker results are averaged over the two sets. StrainSeeker's genus-level sensitivity was 0.968, precision 0.995. False negatives were mostly due to fact that these strains were not present in our database. Identification time was 12.3 minutes.

Sample 2 - mock metagenome consisting of 21 bacteria and a fungus

This sample was used in an early study that proposed to use k-mers for strain identification View publication

StrainSeeker results | Sample in FASTA format | Community composition table ('even' was used)

StrainSeeker accurately identified 20 bacterial strains (Actinomyces odontolyticus is not present in our database, nor are any fungi). Identification time was less than 5 minutes.