Alignment with Genome Studio
I have contigs from a de novo assembly that I want to align against a reference genome to check the accuracy of my assembler. Can Genome Studio be used to do/visualize this?
Thanks
Thanks
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I don't think so
To the best of my knowledge Genome
Studio can not be used to align and view next gen sequencing data. Most NGS alignment tools work on Unix platforms, heavily using command line arguments. You also need to have a good understanding of the alignment process and be able to write small scripts for fine tuning the process. There is a very recent paper in Bioinformatics comparing the NGS aligners from Heng Li et al. I suggest you start there.
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