Hi, I mapped my illumina sequences with one reference bacterial genome and got bam file. Does any guy know what tool I should use to visualize the alignment? And need tutorial for step-by-step bacterial genome alignment or assembly. Thanks.
You can visualize the data using Trackster inside of Galaxy. If you mapped using a built-in genome to Galaxy, there will be a small stacked bar graph icon for your dataset that you can click on to launch the tool, or click on the top menu bar for "Visualization". If you mapped as a Custom Reference Genome, add the .fasta file (same as used for mapping), as a Build under the top "User" menu, then use that in Trackster as the reference.
This wiki link shows where the tutorials and other learning resources from our community are located:
For genome assembly, a local or cloud Galaxy with tools from the Tool Shed (if those of interest are available) will be needed.
Best, Jen, Galaxy team