Bioinformatics ServicesBacterial Isolate Characterization

Genome Assembly – We de novo assemble the genomes of all your isolates from the NGS data. Our process accepts both short and long read data (such as PacBio and Oxford Nanopore). In addition to the genome sequence, we report statistics on assembly quality.

Strain ID & Genome Quality Assessment – The CosmosID database offers the largest collection of multi-kingdom microbial genomic information. The ontology of genomic data in our databases follow the actual phylogenetic hierarchy of genomes, which allows us to place your isolate onto this virtual tree of life with confidence.

Antimicrobial Resistance, Plasmids, Virulence – A detailed characterization of antimicrobial resistance (AMR) genes, virulence factor (VF) genes and Plasmid is carried out using the CosmosID in house pipeline. The CosmosID report is listing identified antimicrobial resistance by drug class and drug, including the identified genes for evidence. Plasmid-borne resistance genes and plasmids are clearly identified.

Multi-locus Sequence Typing (MLST) – We use MLST and similar methods to report sequence type and pathogen-specific genotype information. The MLST allelic profile is predicted for each individual assembly referring to the latest version of MLST databases.

Source-tracking, Transmission, Relatedness – When tracing an outbreak back to its source then SNP trees offer resolution that can make the difference. We compare isolate genomes at full genome-level resolution and establish strain relatedness based on individual SNPs – mutations that arise as an outbreak strains evolves along the chain of transmission events.

Phylogenetic trees are generated using a set of closely related genomes, as well as several representative genomes that we source either from you, from NCBI, or the GenomeTrakr project. For novel organisms and isolates with poorly defined taxonomy we predicted likely taxonomic membership based on Average Nucleotide Identity (ANI) of the isolate genomes and their phylogenetic near neighbors.

Functional analysis – Once your isolate genomes are assembled we identify and annotate coding sequences to reveal the functional potential of your strain.