SOLiD and Velvet 0.7.63

[Magnus]

Hi

I'm trying to run Velvet on SOLiD data. Have done as follows:

Compiled Velvet with color-space support, and increased hash size support.

make 'MAXKMERLENGTH = 50' & color

Creates a data set as follow:

velveth_de Sample20_hash41 41 -short Sample20.csfasta

And then run velvetg_de as follow:

velvetg_de Sample20_hash41

This gives 0 contigs in contigs.fa. Started to check other hash sizes 21, 31 and 41. All resulting in 0 contigs. I know that this data should have some contigs as ~45 % was successfully aligned with MosaikAligner.

I noticed that all sequences in file "Sample20_hash41/Sequences" has the exact same sequence "TAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA". Is this normal?

Did I miss some crucial step?

Best
/Magnus

[KevinLam]

Have you ran the preprocessor and postprocessor and denovoadp scripts from ABI?

[Magnus]

Have you ran the preprocessor and postprocessor and denovoadp scripts from ABI?

No, sorry, I'm new to this (Velvet with color-space). Where can I find information on how to do this?

Best
Magnus

[Chipper]

http://solidsoftwaretools.com/gf/project/denovotools/

[ondovb]

Also check out this thread.