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Showing posts from July, 2016

Behind the scenes with BIOM tables

Today, I'll be covering the BIOM file format , a standardized file format for storing sequence counts in samples.  This file format is typically used in the biological sciences, most notably in amplicon sequencing technologies, such as 16S sequencing. For those of you that aren't as familiar with these technologies.  When we conduct survey studies, we like to get a broad overview of the microbes that are living within a raw sample.  But we don't need to sequence the entire bacteria's genome to identify what the bacteria is.  We can just a sequence a housekeeping gene that every bacteria as - the 16S ribosome. Its a similar strategy deployed in court.  When DNA evidence is presented in the court room, only a tiny, tiny portion of an individuals DNA is actually required to uniquely identify that person. But moving on. The BIOM file format was originally designed to store counts of 16S sequences across samples, but it has grown to become a more generalized file fo