Tool:SamReadViewer - A small utility to visualise read alignment directly from sam format without reference.

Question

[Juke34]

Hello everyone,

For fun I made this little online tool to visualise the alignment of a read in SAM format. It does not require to have the reference. It can maybe have some utility for some of you.

See here: https://juke34.github.io/SamReadViewer/sam2view.html

[Gabriel R.]

nice! maybe point out that you need the MD field to be correct. doesn't it?

[Juke34]

Yes it mentioned on the tool page.
This utility makes it easy to visualise a read alignment against its reference without the reference. Indeed the reference is re-created based on the CIGAR string + the MD tag.
But maybe it is not clear enough.
The tool give also a warning if the MD tag is missing.

[Gabriel R.]

ah great! I only read your biostars post :-)

[Gabriel R.]

very useful little tool btw!

[Juke34]

Thx, I was hoping so but I start to doubt according to the really few feedback I got (from twitter and here)

[Juke34]

Thx, I was hoping so but I start to doubt according to the really few feedback I got (from twitter and here)

[Gabriel R.]

I have coded a subroutine to rebuild the ref. from the CIGAR+MD using htslib, never again! I reuse that code over and over. I would have loved your tool when I was developing my code, it would have saved me a lot of time. I am sure a programmer will enjoy it in the future ;-)

[Juke34]

The code itself to build the ref from CIGAR+MD is from minimap2. So all the credits should go to the minimap2 developers ^^.

Answer 1

[dariober]

Nice! Are you planning to make it a standalone command-line tool? Like to be able to do:

samtools view my.bam | grep 'some-read-name' | SamReadViewer | less

A program I wrote, ASCIIGenome, is in the same spirit but for viewing individual reads yours would be even more streamlined.

[Juke34]

You can already do it using minimap2 appropriate commands. This is just an online implémentation