SOAPdenovo assembly question

Question

[AW]

Hi,

Id be very grateful if someone could help answer my question.

I am interested as to how the flat rd_len_cutoff works in the SOAPdenovo assembly process. It says it only uses the first * bps of each read. My max read is 100bp and minimum 37bp. Therefore, if I set rd_len_cutoff = 100, will it only use 100bp reads OR everything as nothing is longer than 100bp?

Thanks

Alison

[AW]

Hi,

Thanks for your answers, but unfortunately the two answers seem to say different things?

So am I right in saying that if rd_len_cutoff = 100 and my read range is 37-100, no reads will be cut?

And if I remove rd_len_cutoff flag, no reads will be cut?

Thanks

A

[Rayan Chikhi]

yes, actually both answers said the same thing

Answer 1

[Rayan Chikhi]

Everything

Answer 2

[rtliu]

http://soap.genomics.org.cn/soapdenovo.html

4) rd_len_cutof The assembler will cut the reads from the current library to this length.