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One Codex specifications


Unique identifier OMICS_11175
Name One Codex
Interface Web user interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Samuel S. Minot

Publication for One Codex

One Codex citations


Identification of Major Rhizobacterial Taxa Affected by a Glyphosate Tolerant Soybean Line via Shotgun Metagenomic Approach

PMCID: 5924556
PMID: 29659545
DOI: 10.3390/genes9040214

[…] on. The best assembly was selected based on contig N50 and mapping rated, and only those contigs that were longer than 500 bp were kept for further analysis.Metagenomic analysis was also performed by One Codex data platform (hereinafter, One Codex) [] with cloud-based k-mer method, after the compressed FASTQ data, which was appended with .gz, was uploaded to the One Codex platform [], considering […]


Physiological and Comparative Genomic Analysis of Arthrobacter sp. SRS W 1 2016 Provides Insights on Niche Adaptation for Survival in Uraniferous Soils

PMCID: 5793183
PMID: 29324691
DOI: 10.3390/genes9010031

[…] Function Category Comparison tool using IMG/ER. IMG computes top COG hits using RPS-BLAST on PSSM’s provided by CDD. A genome-based phylogenetic tree of strain SRS-1-W-2016 was constructed using the One Codex database platform [], which generates taxonomic classification of nucleotide reads by assessing for exact k-mer matches against their database of bacterial, viral, and fungal genomes, as wel […]


Detection of Spotted Fever Group Rickettsia DNA by Deep Sequencing

PMCID: 5652451
PMID: 29048295
DOI: 10.3201/eid2311.170474

[…] human genome sequences and were filtered out (3,619,386 reads) or were unclassified (8,252 reads). We analyzed the reads for bacterial DNA by using 3 metagenomics tools: Kraken (), PathoScope (), and One Codex ( All 3 analyses returned similar results; ≈80% of classified reads (208/251 reads, 53,958 total nucleotides) matched sequences from SFG Rickettsia spp.; the remain […]


The York Gospels: a 1000 year biological palimpsest

R Soc Open Sci
PMCID: 5666278
PMID: 29134095
DOI: 10.1098/rsos.170988

[…] eted using mapDamage2.0 [] and population genetic PCoA analyses with LASER2.0 []. Metagenomic analyses were completed from host filtered datasets (electronic supplementary material) using metaBIT [], One Codex [] and STAMP []. […]


Comprehensive benchmarking and ensemble approaches for metagenomic classifiers

Genome Biol
PMCID: 5609029
PMID: 28934964
DOI: 10.1186/s13059-017-1299-7

[…] Some authors (listed above) are members of commercial operations in metagenomics, including IBM, CosmosID, Biotia, and One Codex. […]


Lignocellulose Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass Degrading Diversity

PMCID: 5541161
PMID: 28776044
DOI: 10.1128/mSphere.00300-17

[…] or 454 pyrosequencing approaches (, ), resulting in a limited representation of the members of this phylum in sequence databases. Previous analysis of this data set against an earlier version of the One Codex database identified members of the Fibrobacteres as 0.1% of the total metagenome reads (data not shown). However, since this analysis was performed, Rahman et al. () utilized taxonomic binni […]


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One Codex institution(s)
One Codex (Reference Genomics, Inc), San Francisco, CA, USA
One Codex funding source(s)
Supported by the Japan Science and Technology Agency (JST) [the Life Science Database Integration Project conducted by the National Bioscience Database Center (NBDC)].

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