Velvet compilation error

Question

[Sissi]

Hi everyone!

I've been following you since I started working on NGS, but now I need more help :(

I'm trying to assembly long reads derived from 454 and I want to change the MAXKMERLENGTH from 31 to 231 but I got the common message:

Velvet can't handle k-mers as long as 231! We'll stick to 31 if you don't mind.

I know you have been talked about but I can't fix the problem anyway.

If I run:

make 'MAXKMERLENGTH=231' velvetg velveth

on my velvet folder, there are plenty of question and It does not change the make file. I tried then to change directly the make file as suggested, but still nothing. If I run:

which velvetg

I got /usr/bin/velvetg but I don't find the file in this folder!

I tried to change the length with 219, then back to 231 and If I run the velvet I still get the 219.

I hope I explained my self, I'm still a newbie in bioinformatics.

[SES]

Try just the make command with the kmer variable without the velveth/g. Also, 231 is really high. You would have to have long reads and a very high coverage for that to produce a useful assembly.

[Sissi]

Hi Ses, thanks for your answer.

I tried with or without velveth/g after make 'MAX..", with or without make clean, with or without make velvet/h afterwards.

I changed the length to 151, but still the same error message..(My reads are around 400bp btw).

Edit.

There is a problem with make and getwd. I'm working on that ;)