VITCOMIC2 is a visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing.


Try VITCOMIC2

Metagenome/16S rRNA gene Amplicon Sequencing FASTA/FASTQ file:
File format: FASTA flat FASTQ flatFASTA gzippedFASTQ gzipped
Conduct 16S rRNA gene Copy number normalization?: No Yes
Conduct 16S rRNA gene Assembly? (Shotgun metagenome only): No Yes
ID: (use [A-Za-z0-9-_])
Email:

How to use

1. Input data
Both of a FASTA/FASTQ file and gzipped FASTA/FASTQ file are acceptable for the input data in the VITCOMIC2. Sample 16S rRNA gene Amplicon sequencing fastq data. Rich text file (e.g., MS Word docx, doc, rtf file) is not acceptable.
2. File format
File format is a file format identifier of your FASTA/FASTQ file. To reduce the size of your file, we strongly recommend that you compress your file with gzip. If you don't compress your file, please choose "flat file".
3. ID
ID is a identifier of your upload file. Please input any alfabet and number such as "Sample1".
4. Email
Please input your Email address. This Email address is very important because the URL of your VITCOMIC2 result is send by the Email after calculation (usually less than one hour).
Reference SSU rRNA gene sequence DB
A FASTA file of the VITCOMIC2 reference SSU rRNA gene sequence DB can be downloaded from here. Genus and Phylum information of each sequence in the reference DB can be obtained from here. These sequence data were originally obtained from RDP (Ribosomal Database Project) and CRW (Comparative RNA Web site).
Reference 16S rRNA gene copy number sequence DB
A FASTA file of the VITCOMIC2 reference 16S rRNA gene copy number sequence DB can be downloaded from here. These sequence data were originally obtained from NCBI Genome DB.
Reference Type strain 16S rRNA gene sequence DB
A FASTA file of the VITCOMIC2 reference Type strain 16S rRNA gene sequence DB can be downloaded from here. These sequence data were a subset of the VITCOMIC2 Reference SSU rRNA gene sequence DB.

Reference

Mori H, Maruyama T, Yano M, Yamada T, Kurokawa K, VITCOMIC2: visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing. BMC Systems Biology. 12 (Suppl 2):30.
Journal web site.