[Credits]

Life Science Database Archive
MicrobeDB.jp

SRA

Data detail

info Data name SRA
info DOI 
info Version 
V2
V1-
info Description of data contents 

Metadata and taxonomic/functional compositions of 16S rRNA gene-based amplicon sequencing and metagenomic shotgun sequencing samples. Metadata were annotated by several ontologies (i.e., MEO, MSV, and NCBI Taxonomy).
Data file (compressed in tar.gzip) consists of some directories (see the following table).

info Data file 
File name:
sra.tar.gz
File URL:
https://dbarchive.biosciencedbc.jp/data/microbedb/LATEST/sra.tar.gz
File size:
8.4 GB
info Simple search URL -
info Data acquisition method 

Metadata and DNA sequence data of each 16S rRNA gene-based amplicon sequencing and metagenomic shotgun sequencing sample were obtained from INSDC DRA/ERA/SRA.

info Data analysis method 

After quality filtering of reads, DNA sequence data of all 16S rRNA gene-based amplicon sequencing and metagenomic shotgun sequencing samples were phylogenetically analyzed by VITCOMIC2. Functional composition of metagenomic shotgun sequencing samples were analyzed by the combination of MetaGeneMark, GHOSTX, and Refsequences database.

info Number of data entries 

1,926,303,942 triples

Data itemDescription
sra/metadata/meo_mapping/ The MEO annotation results of 16S rRNA gene-based amplicon sequencing and metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA.
sra/metadata/msv_mapping/ The MSV annotation results of 16S rRNA gene-based amplicon sequencing and metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA.
sra/metadata/host_taxonomy_mapping/ The NCBI Taxonomy annotation results of host organisms of microbes for 16S rRNA gene-based amplicon sequencing and metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA.
sra/metadata/sra_description/ The metadata descriptions of 16S rRNA gene-based amplicon sequencing and metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA.
sra/analysis/sra/function/mbgd/ The MBGD ortholog cluster composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA.
sra/analysis/sra/function/mgfo/ The MBGD ortholog functional composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA.
sra/analysis/sra/function/ko/ The KEGG ortholog composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA.
sra/analysis/sra/function/pathway/ The KEGG pathway composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA.
sra/analysis/sra/taxonomy/ The taxonomic composition of 16S rRNA gene-based amplicon sequencing and metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA.
sra/analysis/env/function/mbgd/ The MBGD ortholog cluster composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA that were annotated to each MEO category.
sra/analysis/env/function/mgfo/ The MBGD ortholog function composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA that were annotated to each MEO category.
sra/analysis/env/function/ko/ The KEGG ortholog composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA that were annotated to each MEO category.
sra/analysis/env/function/pathway/ The KEGG pathway composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA that were annotated to each MEO category.
sra/analysis/env/taxonomy/meta16s/ The taxonomic composition of 16S rRNA gene-based amplicon sequencing samples in INSDC DRA/ERA/SRA that were annotated to each MEO category.
sra/analysis/env/taxonomy/metagenome/ The taxonomic composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA that were annotated to each MEO category.