You can already do it using minimap2 appropriate commands. This is just an online implémentation
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Tool: SamReadViewer - A small utility to visualise read alignment directly from sam format without reference.
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
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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.
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nice! maybe point out that you need the MD field to be correct. doesn't it?
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.
ah great! I only read your biostars post :-)
very useful little tool btw!
Thx, I was hoping so but I start to doubt according to the really few feedback I got (from twitter and here)
Thx, I was hoping so but I start to doubt according to the really few feedback I got (from twitter and here)
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 ;-)
The code itself to build the ref from CIGAR+MD is from minimap2. So all the credits should go to the minimap2 developers ^^.