“What’s the Answer?” Thread

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

BioStar Question of the Week:
With the advent of NGS data, lots of people have been looking for ways to visualize the BAM and SAM files for further analysis. We’ve been coming across that a lot in our workshops lately. I think you might be able to do that pretty well with a custom track at UCSC Genome Browser, though it’s probably not as simple as some tools listed and sometimes you need more. Today’s biostar question and answer:

…I want to know is there any freely available software for the visualization of the aligned reads including their sequences for Bowtie output (sam or bam format)….

Highlighted Answer:
The most up-voted answer was a simple one sentence:

See this great blog post reviewing several NGS genome viewers (they all read BAM format).

(It is a great blog post). There are other answers too that were helpful, check out the discussion…