maximum distance of 8 - Githubissues

gui11aume / starcode

All pairs search and sequence clustering

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maximum distance of 8 #12

Open claudiuskerth opened 8 years ago

claudiuskerth commented 8 years ago

Would it be possible to allow starcode to run with greater distances than 8?

I haven't observed excessive memory usage or running times with --dist 8 and my data yet (several 100,000 50bp long reads).

I would like to detect within species homologous sequences and would like to allow greater divergence than 8 for my 100bp long reads.

many thanks

claudius

claudiuskerth commented 8 years ago

Hi Eduard,

sorry to bother you with this, but do you intend to implement that "enhancement" any time soon. Don't worry if not. I will just have to resort to blast.

cheers

claudius

ezorita commented 8 years ago

Hi Claudius, for now this enhancement is not in our plans since it involves a major recoding. I will definitely let you know whenever we start implementing it.