I am working on next generation sequencing Illumina platform. 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). or software which can read fastq file format.
Edit (md): I was thinking about some requirements for such software:
- Reliably read sam, bam, vcf, and ace, wig files
- Visualization of inserts, deletion, mismatches in the alignments
- Support for visualization of gene models and annotation data in various formats including genbank, embl, gff. For example, if I found my gene of interest I would like to visualize all reads covering a certain part, promotor region or exon.
- Therefore: easy quick navigation in the reads and in the reference annotation data
- ability to view several tracks at the same time
- something like a desktop version of UCSC genome browser + read pilup like in IGV
I think it is possible to do these things with some of the libraries, or partially with some of the desktop tools. But to take a good quick look most tools lack some features.
You notice the contradictions in your question right?
It seems to be a good question though, because a good and easy to use app is missing.