SAM/BAM files (Assembly Browser). The main goal of the Assembly Browser is to let a user 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 Browsesr window appears:

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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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