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SAM/BAM files (Assembly Browser).  Assembly Browser is used to visualize and 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:


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.



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