What are your preferred programs for processing DNA long reads? (de novo assembly)

Question

[ExtentHonest56]

Gathering information for programs and assemblers used for DNA de novo assembly with long reads. Hoping to publish a libguide to help students around our campus. If you have done de novo assembly with long reads, what is your favorite assembler you used and why? What was the sequencing company you used? What organism type were you working with (plants, bacteria, mammalian, etc.)? What other programs did you use that helped while processing these reads (overlap detection, polishing, scaffolding, etc.)? Any and all information is appreciated!

I have found many programs and assemblers while researching this, but since I have personally never done de novo assembly with long reads, I am hoping to get input from those that have.

[Medhat]

There is already an article about the topic that was recently published (I was one of the individuals approached to contribute to this article). You can find the article titled "Variant Analysis and Genome Assembly: Recommended Tools for Next-Level Sequencing Analysis" at the following link:

https://www.seqanswers.com/articles/324604-variant-analysis-and-genome-assembly-recommended-tools-for-next-level-sequencing-analysis

Answer 1

[colindaven]

You won't find a more exhaustive list of assemblers (up to date in mid 2023) then this:

https://github.com/nadegeguiglielmoni/genome_assembly_tools

[GenoMax]

Interestingly shasta (LINK) is missing from this list. You recommended that program in past threads.

[colindaven]

Very good point, I've informed the authors

[ExtentHonest56]

Thank you, this is extremely helpful! I found this also in my reading, as I'm currently focusing more on long read processing (gathering information for short, long, and hybrid de novo). Thought it was neat, so wanted to share for anyone that comes across this post.

https://long-read-tools.org/tools