The One Codex Blog

Length bias - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4643231/ Choice of primers and library prep - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381044/ Choice of primers - http://www.ncbi.nlm.nih.gov/pubmed/26271760

We are happy to say that we’ve just released a new and improved reference database! Here are a few highlights of the things we’re proud of.

Spanning the tree of life

We’ve increased our coverage of Eukaryotes, with 874 fungal genomes and 133 protists, including 8 strains of Toxoplasma gondii and our first reference of Geotrichum candidum. We’ve also added a number of fungal and protozoan pathogens: we have two times the number of Plasmodium falciparum and three times the number of Trichophyton rubrum.

Today we’re happy to announce two new features for all users on One Codex: whole genome clustering and integration with Illumina’s BaseSpace. The first opens the door to new types of analyses, while we hope the second will allow many to spend less time moving their data around and more time exploring it!

Whole (meta)genome clustering

In addition to our previous sample comparison tool, we’re very excited to announce that One Codex now supports arbitrary, interactive exploration and clustering of your isolates and metagenomic samples. This cluster view (login/free registration required) enables rapid, reference-free exploration and comparison of NGS samples, often both highlighting expected similarities and revealing important inter-sample differences.

Ok, anthrax might sound a bit scary, but this is a story about something that should make you feel good.

Wait, is that really Anthrax?

Back in the Spring of 2015, researchers studying the microbial ecology of the built environment generated a very large amount of genomic data from microbes found in the New York City subway system. To give you some idea of the magnitude, they generated 10.4 billion sequence reads across 1,457 samples. That’s a lot of microbiome data.

Today we added automated Multi-Locus Sequence Typing (MLST) to One Codex.

MLST is a powerful epidemiological tool that is based on curated collections of conserved mutations in core marker genes. This common reference standard is used to differentiate closely-related isolates of the same species, with many common species having hundreds or thousands of defined MLST profiles.

Datasets that are identified as being isolates or single-genome assemblies will be automatically analyzed and tagged with the detected ST label. This MLST tagging is implemented for the most commonly analyzed bacteria, including E. coli, S. enterica, and L. monocytogenes.¹