Scott Cain1/n I just want to take a moment to shout out to the State Public Health Bioinformatics group (STaPH-B #STaPHB) for outstanding work. Several months ago, I wanted to try out #minimap2 for something, so I went looking for a published Docker container and found https://hub.docker.com/r/staphb/minimap2 which worked great. Yesterday, it occurred to me that I wanted to do something a little additional and could just add what I wanted to the existing Dockerfile, so I went looking for it...
@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 :-)
Joseph Guhlin#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
Steven Van BelleghemBeen 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/
naturepokerSo - 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?
Nicola RomanòIs 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
New update to the #minimap2 #rust crate. Experimental multithread support.
