Hey there… I have a bacterial genome NGS reads please help me to assemble these reads for further process
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Good day Waqas. I recommend using Torsten Seeman’s Shovill tool - this is a wrapper around SPAdes and does a very good job with most microbial genomes. Also note that the Microbinfie Podcast discusses Microbial Genome Assembly in episodes 19, 20 and 22. All of these are worth a listen.
Finally there are some tutorials on the Galaxy Training portal on Assembly (although I would not use Velvet as used in their examples, Shovill is much better) and Annotation with e.g. Prokka.
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