SAM/BAM files (Assembly Browser). The main goal of the Assembly Browser is is used to let a user visualize and efficiently browse efficiently browse large next generation sequence assemblies. Currently supported formats are SAM (Sequence Alignment/Map) and BAM, which is a binary version of the SAM format. Both formats are produced by SAMtools and described in the following specification: SAMtools. To activate the Alignment Editor open any assembly file. For example you can use the $ugene/data/samples/Assembly/chrM.bam file provided with UGENE. After opening the file in UGENE the Assembly Browser window appears:
HTML |
---|
<center> <br> <img src="/wiki/download/attachments/2883702/assembly.gif"/> <br> </center> |
Using the Assembly Browser you can:
...
browsing and zooming assembly
...
, getting information about reads
...
, short reads vizualization
...
, associating reference sequence
...
, consensus sequence, exporting.
Example 3: Highlighting the strand of reads. You can do this using the context menu or the Options Panel.
HTML |
---|
<center> <br> <img src="/wiki/download/attachments/2883702/assembly_strand.gif"/> <br> </center> |