Tool:SamReadViewer - A small utility to visualise read alignment directly from sam format without reference.
1
4
Entering edit mode
12 months ago
Juke34 ★ 6.3k

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

screenshot

sam viewer read Tool • 606 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

very useful little tool btw!

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 ;-)

ADD REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
8 months ago

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.

ADD COMMENT
1
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 2727 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6