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 »
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.
How to get easy-to-install software from the Biocontainer community project!
The NCGAS team finds that many users unfamiliar with SRA-Toolkit or the command line struggle with configuring the program or parsing its multiple commands and options. Here, I aim to condense and distill this information so that a beginner can use the SRA to their heart’s content!
Visualizing the distribution of scaffold size in an assembly is a nice complement to basic summary statistics. In this blog post, I’ll describe how to plot a histogram of scaffold lengths, using the new mOrnAna1 platypus assembly as an example.
An updated comparison in reference to de novo genomes
Thinking about doing a genome project? This technical paper outlines a good place to start, as well as what software to look into, and brings up some important considerations.
How to run the assembler software canu on IU’s Carbonate Cluster
Plants get their time in the spotlight with two new chromosome scale assemblies
UPDATE: This information has been updated for 2019! See our new blog here! UPDATE: My good friend at BioNano gave me some updated stats for their services. See the update on the Bionano introduction as well as the updated Comparison Table! Contents Short Introduction to the Technologies Comparison Table Important Considerations General Guidelines Other Analyses Sources…… Read more »