What Does The 'Readsinfofile' Option Require When Using Soapdenovo 2 With The Multikmer Method

Question

[AW]

I want to use the multikmer method in SOAPdenovo2. I understand that I set the max kmer with -m in the contig step. However, I noticed the -s option that seems necessary with this option. What does the readsInfoFile refer to?

 -m <int>         max k when using multi-kmer, and the parameters below are used along with multi-kmer, [NO]
 -s <string>      readsInfoFile:The file contains information of solexa reads(It's necessary when using multi-kmer)

Thanks very much, any help would be much appreciated.

Alison

Answer 1

[Istvan Albert]

I think the answer can be found on the help page, although not readily apparent.

The option appears to require a file that is called config_file see entry called 1. Configuration file that says among other things:

The configuration file tells the assembler where to find these files and the relevant information. "example.config" is an example of such a file.