@thebiologistisn I was thinking about the comparison of 2 similar assemblies and came up with a potentially useful visualization. As a test set I used the C. elegans N2 assembly (original) and the VC2010 assembly (a resequencing of the same strain, so it should be very similar). I already compared these 2 with #minimap2 and have that data on #WormBase's #JBrowse2. I wrote a simple script that would take a sorted paf file (minimap2) and find gaps. This is the result: https://wormbase.org/tools/genome/jbrowse2/?session=share-SSR4hA6gzo&password=TFpjE

@thebiologistisn oh, well, I’m not an expert on comparative genomics, but I do like #minimap2, mostly because it’s easy, fast and gives reasonable looking results for C. elegans and friends. And, not surprisingly, makes nice looking pictures in #JBrowse2 When I get back to my laptop, I’ll post some pictures (still don’t do much genome browsing on my phone :-)

#Minimap2 #Rust library release: minimap2 v0.1.13+minimap2.2.26

* Latest minimap2 stable release (2.26)
* with_seq function
* hopefully compiles for MacOS / aarch64.
* Still struggling with SSE, I recommend using simde feature
*Soft-clipping properly in CIGAR strings but use caution. Happy to work on it more.

https://github.com/jguhlin/minimap2-rs

https://crates.io/crates/minimap2

And the -sys crate
https://crates.io/crates/minimap2-sys

#bioinformatics #genomics #nanopore #pacbio

Been working on a #pangenome tutorial comparing alignments with #minimap2 (left) and #seqseqpan (right) and adding genome features, including species-specific sequences, sequence similarity, TEs, and ATAC-seq (data from Heliconius butterflies). https://stevenvb12.github.io/

RT @JosephGuhlin
#Minimap2 library for #Python: https://pypi.org/project/minimappers2/

Very alpha stage, but has multithreading. Results are returned in DataFrames with @DataPolars (easy convert to Pandas).

Feedback appreciated. I don't know what platforms it'll work on.

#Bioinformatics #Genomics #Nanopore

So - with kit v14 and what seems to be pretty great #nanopore read qualities across the board (still itching to test out duplex calls on existing data and compare), should we reconfigure #minimap2 options for longread mapping? Or would using asm5 preset suffice?

Anyone with v14 reads with some insights?

#bioinformatics #sequencing #genomics

RT @Saurabh_Kalikar@twitter.com

@sanchit_misra@twitter.com @chirgjain@twitter.com @wasim_galaxy@twitter.com @lh3lh3@twitter.com As promised, we are excited to release mm2-fast-v1.0, the first production ready version compatible with latest minimap2 v2.24 and up to 1.8x faster. https://github.com/bwa-mem2/mm2-fast/releases/tag/mm2-fast-v1.0
@sanchit_misra@twitter.com @wasim_galaxy@twitter.com @lh3lh3@twitter.com @chirgjain@twitter.com #minimap2 #longreads #HPC #genomics

🐦🔗: https://twitter.com/Saurabh_Kalikar/status/1605529044224598018

Is there any one familiar with analysis of #nanopore #longreads ?

I'm having some bizarre issues when using #minimap2 to align them and I'm almost out of ideas of what to try next...

Here's an explanation of my issue

https://www.biostars.org/p/9546698/

#sequencing #alignment #bioinformatics

RT @JosephGuhlin@twitter.com

New update to the #minimap2 #rust crate. Experimental multithread support.

https://crates.io/crates/minimap2

🐦🔗: https://twitter.com/JosephGuhlin/status/1592333503357935616

New update to the #minimap2 #rust crate. Experimental multithread support.

https://crates.io/crates/minimap2

#bioinformatics #genomics