Why Nanopore Just out (March 1st 2021): New nanopore sequencing chemistry in developers’ hands; set to deliver Q20+ (99%+) “raw read” accuracy (modified enzyme, tweaked run conditions and further improved base calling model in the Bonito base caller) Nanopore reads are much longer than PacBio, they can reach 330 kbp in length, even exceeding 2Mb. Yield/cell is 245Gb. It can be used for both…… Read more »
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NCGAS Service Changes
Changes to NCGAS services – starting December 31, 2021
Introduction to Illumina Sequencing
NCGAS is teaching a course in genomics, called GEMS: WORKFLOWS IN GENOMICS. GEMS is Genomics and Eco-evolution of Multi-scale Symbioses. Included in all this are short introductions to Illumina and Nanopore sequencing. I thought I would give these to you as blogs, this one on Illumina and another to come on Nanopore, and eventually one on PacBio. Note that we recently posted a blog on next generation sequencing, i.e. long read sequencing methods. That has a different flavor from what I’m doing here.
Circle-sequencing RNA
We hosted Jean-Francois Gout of Mississippi State University this month. Jean-Francois did his post-doc work with the Lynch Lab at Indiana University and then Arizona State University (when the Lynch Lab relocated). He spoke about RNA transcription error and how to detect and study them using novel circle-sequencing of the RNA to produce multiple copies…… Read more »
Tunneling a Jupyter Notebook from an HPC
Jupyter Notebook Tunneling is a convenient trick to have in your back pocket, especially when the resources on your personal computer are limiting your progress. Tunneling allows you to run your notebook from a remote host such that your processes utilize the resources available on your host, rather than your personal computer. In this brief…… Read more »
A Quick Intro to Singularity Containers
What is Singularity? A Singularity container is used to encapsulate all required software and dependencies for a workflow. This is extremely useful when trying to execute a particular workflow on different systems. Containers make compiling software on different compute platforms easy and effortless. The best part is you don’t need admin privileges with Singularity if…… Read more »
Finding protein homologs at NCBI and making a phylogenetic tree
This blog is brought to you by NCGAS undergraduate intern Christina Campbell and is inspired by the curiosity of former NCGAS Co-PI Craig Stewart (who is now enjoying well-earned retirement). This is part of a multi-part series on exploring questions about epigenetics in beetles. Follow along as we determine which species have methylation enzymes, how these patterns are organized on the species tree of beetles, and how you can explore possible patterns of methylation – entirely with bioinformatics!
Celebrating what we can about 2020
2020 was a rough year for many reasons, but there are still things to be excited about – here are the staff picks of interesting or exciting news in 2020!
Preparing for the approaching retirement of DC2
The Data Capacitor II or DC2 (for more details, link here) is a high-performance file system that will be retiring soon. Toward that end, on October 11th, 2020 the file system will become read-only and on December 11th, 2020 the file system will be shut down for the last time. This will affect all users…… Read more »
Installing Jupyter notebook on Jetstream
Jupyter notebook is an open-source project that supports interactive data science and scientific computing across programming languages. Notebooks are great to have all your code, text, images, and equations in one single document. This is easy to share, run on other datasets, and customize scripts from a template. This tutorial is on how to setup…… Read more »