https://livingsystems.cc/tags/16s-sequencing/ Recent content in 16s-Sequencing on Living_Systems Hugo en-us Fri, 25 Sep 2026 16:47:12 +0200 https://livingsystems.cc/posts/lrhq-speeds-up-alignment-in-emu/ Fri, 25 Sep 2026 16:47:12 +0200 https://livingsystems.cc/posts/lrhq-speeds-up-alignment-in-emu/ <p><a href="https://github.com/treangenlab/emu" target="_blank" rel="noopener">Emu</a> is a popular read classifier and abundance estimator for 16S sequencing (sequencing of the 16S ribosomal RNA subunit, which is a common method for determining the abundance of bacteria in a sample, typically at the granularity of genus and/or species). We use it as part of the <a href="https://github.com/genomic-medicine-sweden/trana" target="_blank" rel="noopener">Trana pipeline</a> for a selection of 16S sequencing samples at the Karolinska Hospital.</p> <p>Emu was specifically created to account for the generally lower accuracy of Oxford Nanopore (ONT) reads. Although this situation has drastically improved in recent years, with new flow cells and basecalling models, the error rate still typically remains around 1%, which, especially for a very sensitive analysis like 16S sequencing, is significant.</p>