[Beginner] Whole Genome Sequence Assembly: Where do I start?
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3 months ago
apcreyes29 • 0

Hi! I'm a graduate student and I want to learn how perform genome assembly and annotation but I know very little about it. I'm also a beginner at coding and I've been learning Python so far. Where do I start learning? Are there any programs that's friendly for beginners? I've also learned recently about usegalaxy.org. Are the programs in that site worth using for genome assembly and annotation? Thank you.

sequencing whole genome beginner assembly annotation • 182 views
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3 months ago
liorglic ▴ 880

Your question is a bit broad, so it would be hard to give precise answers. Generally speaking, I'd start by reading some of the many tutorials about genome assembly that you can find by simply googling it. You can also look at some review papers from recent years. There are some factors that will determine the tools that you will end up using, mainly the organism (bacteri vs. eukaryotes), genome size, and type of sequencing data (short vs. long reads, sequencing depth).
As for genome annotation - this is a more difficult topic, but what I wrote above generally applies too. Check out this review for instance.
Regarding Galaxy - if the online tools there do what you want, then by all means go ahead and use them. Other options include command-line tools and software. Most likely you won't have to write much code of your own to perform genome assembly and annotation. If this is the first time you are doing computational work, you may want to have someone more experienced to help you get started.

Good luck!

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