Identification

Can EzBioCloud Genome Identification be used for metagenomic samples?

No, EzBioCloud Genome Identification is designed for the analysis of bacterial genomes, not metagenomic samples. For metagenomic samples, use EzBioCloud Shotgun Microbiome or Clinical Metagenomics.

What are the system requirements for using EzBioCloud Genome Identification?

EzBioCloud Genome Identification is a web-based service that can be accessed using a web browser on any device with an internet connection.

How is the quality of the input sequencing data assessed by EzBioCloud Genome Identification?

The quality of the input sequencing data is assessed using basic statistics such as the number of reads, genome size, G+C content, and assembly N50 length. The quality of the genome assembly is assessed using additional metrics such as UBCG recovery and RRS/CSS scores.

What is the positive/negative marker decision in the pathogenicity markers section of the EzBioCloud Genome Identification report?

The positive/negative marker decision provides a summary of the detected pathogenicity markers and their association with different pathogenicity categories. The decision indicates whether the input genome sequence is positive or negative for each marker, and provides an overall classification of the pathogenicity of the isolate.

What is UBCG recovery in the genome sequence quality section of the EzBioCloud Genome Identification report?

UBCG recovery refers to the percentage of universal single-copy bacterial genes (UBCGs) that were identified in the input genome sequence. This metric provides an estimate of the completeness of the genome assembly.

What is the normal range for genome size and G+C contents in the EzBioCloud Genome Identification report?

The normal range for genome size and G+C contents is based on the reference database used for comparison in the ANI analysis.

What is included in the EzBioCloud Genome Identification report?

The EzBioCloud Genome Identification report includes a summary of the sequencing read quality, genome sequence quality, species identification, MLST results, antibiotic resistance determinants, and pathogenicity marker detection.

What is MLST?

MLST (multi-locus sequence typing) is a method for characterizing bacterial strains based on the sequence of several housekeeping genes. EzBioCloud Genome Identification uses the MLST tool to assign a sequence type (ST) to the input genome sequence based on the MLST schemes released through the PubMLST repository.

How does EzBioCloud Genome Identification detect pathogenicity markers?

EzBioCloud Genome Identification includes custom curated pathogenicity marker schemes for several clinically important pathogens, including Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus. The schemes include detection of genetic markers associated with different pathogenicity categories, such as toxin production or antibiotic resistance.

How does EzBioCloud Genome Identification predict antibiotic resistance?

EzBioCloud Genome Identification uses the AMRFinderPlus tool to identify antibiotic resistance determinants in the input genome sequence. The tool searches for genes associated with antibiotic resistance, and provides a summary of the number of resistance factors present for each antibiotic class and subclass.

What is ANI analysis?

ANI analysis is a method for comparing the similarity of two bacterial genomes based on the average nucleotide identity of their shared genes. EzBioCloud Genome Identification uses ANI analysis to compare the input genome sequence to a database of reference genomes to determine the species of the input genome.

How does EzBioCloud Genome Identification identify bacterial species?

EzBioCloud Genome Identification uses a combination of average nucleotide identity (ANI) analysis and 16S rRNA gene sequencing to identify bacterial species.

What types of input data does EzBioCloud Genome Identification support?

EzBioCloud Genome Identification supports Illumina, Nanopore, and PacBio sequencing data, as well as pre-assembled genome sequences in FASTA format.

What is EzBioCloud Genome Identification?

EzBioCloud Genome identification is a web-based service that analyzes bacterial genome sequences to identify species, predict antibiotic resistance, and detect pathogenicity markers.