Determination of longest read-SOAPdenovo2

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7.5 years ago

eischzj12 • 0

I'm working on using SOAPdenovo for short-read assembly. How do you determine the length of your longest read? I want to set this equal to the rd_len_cutoff.

Thanks

soapdenovo2 read length Assembly • 1.3k views

ADD COMMENT • link 7.5 years ago by eischzj12 • 0

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You can run stats.sh from BBMap on your dataset to get that information. What kind of data is this?

ADD REPLY • link 7.5 years ago by GenoMax 141k

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Paired end Illumina sequence data. Sorry for being vague, I'm not very familiar with the relevant information to provide. Still learning the ropes. BBMap is something I need to download separately then I take it?

ADD REPLY • link 7.5 years ago by eischzj12 • 0

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I have linked BBMap in post above.

If your illumina sequencing was done for say 150 cycles (you would have 150 bp reads in that case) then the length of your longest (and perhaps all reads, if they have not been trimmed) would be 150.

ADD REPLY • link 7.5 years ago by GenoMax 141k

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