Hi
I have been having a go at running different assemblers on a variety of bacterial genomes. So far Velvet and Abyss have been very simple to use and have given me some useful output. I am however having trouble with some of the other assemblers and I was hoping someone out there might be able to help.
SOAPdenovo
After having obtained the version from the author that allows kmer values of greater than 31, I tried running it on a 2.5mb genome consisting of 54 bp Illumina reads. Using a kmer value of 47 (obtained using the velvet optimisation script) and run successfully using Velvet and Abyss, I tried to run SOAPdenovo. However, I immediately ran into trouble as the memory requirements exceeded 30gb and my job was cancelled automatically. Is this to be expected with higher kmer values and SOAP?
SSAKE
I typically use fastq files that have already been quality filtered. Is there a way of feeding these directly in to SSAKE. I may be being slow but it wouldn't accept fastq files...
ALLPATHS
Is it possible to run the assembler without a jumping library?
Any help would be gratefully appreciated.
I have been having a go at running different assemblers on a variety of bacterial genomes. So far Velvet and Abyss have been very simple to use and have given me some useful output. I am however having trouble with some of the other assemblers and I was hoping someone out there might be able to help.
SOAPdenovo
After having obtained the version from the author that allows kmer values of greater than 31, I tried running it on a 2.5mb genome consisting of 54 bp Illumina reads. Using a kmer value of 47 (obtained using the velvet optimisation script) and run successfully using Velvet and Abyss, I tried to run SOAPdenovo. However, I immediately ran into trouble as the memory requirements exceeded 30gb and my job was cancelled automatically. Is this to be expected with higher kmer values and SOAP?
SSAKE
I typically use fastq files that have already been quality filtered. Is there a way of feeding these directly in to SSAKE. I may be being slow but it wouldn't accept fastq files...
ALLPATHS
Is it possible to run the assembler without a jumping library?
Any help would be gratefully appreciated.
Comment