EzBioCloud offers the following applications for microbial genomics:
This service was previously found under the “Identify” menu. Input data is a single 16S sequence from Bacteria or Archaea, and the output is a list of search hits of known species or carefully selected phylotypes with pairwise sequence similarities. This service has been published and cited over 7,500 times. The database is a compilation of public data and in-house data generated using PacBio full-length 16S sequencing. It is intended to be used for academic purposes. If you are using this for quality-control, industrial validation, or clinical uses, we recommend the TrueBac ID-16S service.
This service provides genome-based identification of Bacteria and Archaea from input data that is either FASTA format sequence, for assembled contigs, or as raw unassembled NGS data in FASTQ format. The output is a list of hits with highest average nucleotide identities (ANI), and with definitive identification at the species or subspecies level. It also provides a list of antibiotic resistance and pathogenicity-related genes predicted from the genome sequence. It is a paid service due to the significantly high computing (cloud) cost. However, we would be happy to offer this service to academic users if the data is immediately used in a publication. (please contact us at email@example.com for details).
16S-based MTP (Microbiome Taxonomic Profiling)
This service provides comprehensive bioinformatics analysis on NGS sample data from 16S gene microbiome surveys. Input data can be either FASTQ Illumina paired/single end file(s) or FASTA files. The output is a taxonomic profile which consists of counts and identification of each 16S sequence in the microbiome sample. Users can explore community structure and perform various bioinformatics on single samples and groups of samples. Major functionality includes alpha-, beta-diversity, biomarker discovery (LefSe) and functional prediction from taxonomic profiles (PICRUSt). It uses the EzBioCloud’s database instead of out-dated, inaccurate crowd-sourced public databases. Academic users are given a free community license allowing the upload of up to 200 samples (this number is subject to change without notice). With the systematic taxonomic organization and high quality of reference genome assemblies in the EZBioCloud users of our MTP service can expect much better species level resolution of their microbiome samples. They can also expect more accurate relative abundance measures and statistics since data can be normalized to known 16S gene copy numbers that we derive from the reference genome assemblies.
Shotgun-based MTP (Microbiome Taxonomic Profiling)
This service provides comprehensive bioinformatics analysis on NGS data from shotgun sequencing of microbiome samples. Input data is in FASTQ format files and the output will be an accurate taxonomic profile of the sample at the species or subspecies level. This service is currently under development and will be released soon. If you want to become a beta tester, please contact firstname.lastname@example.org. It uses the EzBioCloud genome database in which all reference genomes were correctly identified using the TrueBac ID system. For example, Ruminococcus sp. 5_1_39BFAA genome will be recognized correctly as Blautia wexlerae, instead of Ruminococcus [Learn more].
WG (Whole Genome Analysis)
This service provides a comprehensive bioinformatics analysis on a single bacterial genome. The input data is either assembled contigs/scaffolds in FASTA format or raw, unassembled NGS data in FASTQ format. The output is a completely annotated genome of the bacterium, and other information such as taxonomic identification and functional statistics. Users can browse the genome, or search by genes and BLAST both. Please see here for an example. The users are free to browse all genomes in the EzBioCloud. If you want to upload your own genome into the system, please contact email@example.com.
CG (Comparative Genomics)
The best way to understand the genome of an organism is to compare it with others. Our Comparative Genomics service provides comparative analyses of gene content, pan- & core-genome sets, phylogenomics, and biomarkers such as differentially present genes and much more. We aimed to provide sufficient on-demand, interactive bioinformatics for those who want to mine data from multiple genome sequences. The best way to understand this comprehensive bioinformatics service is to try this tutorial.
Last updated Sept. 16, 2018