Hash Table

[lvogel]

Hi all,
I am a total beginner with bioinformatics, and I am supposed to build a hash table. I have been reading up on everything (stampy, shell scripts, etc.), but nowhere can I find simple guidlines on how to build a hash table. Yes, I know the code to use to execute the command in Python; I just need to know how do I figure out what length to use for k-mers, etc.
We have many short reads from Illumina MiSeq, and I built a genome already, based on Genbank data.
I am getting nowhere anymore with searching the Internet, so I would really appreciate some help.
Thanks!

[dpryan]

Perhaps you could tell us exactly why you're trying, as a beginner, to do this sort of coding. There are many many aligners already written and you can feed them pretty much any reference sequence you want. Why not just save yourself the hassle and use one of them?

[lvogel]

Re: hash table

Thank you so much for taking the time to answer. Actually, I think you're probably right. The supervisor I'm doing research with expects me to mostly figure things out for myself. I asked her about it, but she tells me only to read the readme file for stampy, which I have, and that just shows a general example of how to use the command with -H

When I go into the proper directory of the server and type ls, I don't see anything that looks like it could be used for a hash table.

Perhaps you can point me in the direction of some pre-written aligners on the web?

Many Thanks

[GenoMax]

http://bib.oxfordjournals.org/content/11/5/473.full