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: 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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