Assembling, browsing and analyzing of short reads assemblies
3. SAM/BAM files (Assembly Browser). If you open a file with a short reads assembly, like BAM or SAM files you see the following picture 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:
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<center> <br> <img src="/wiki/download/attachments/25234292883702/pic13assembly.pnggif"/> </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.
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<center> <br> <img src="/wiki/download/attachments/2523429/pic14 (3).png2883702/assembly_strand.gif"/> <br> </center> |