Hi,
I'm a beginner to the field of sequence analysis.
I'm currently working on assembly of diploid fugal genome which is around the sizes of 60Mb. Sequenced using Illumina HiSeq2000. I have used Velvet assembly software to construct contigs. However, it ended up in more than 100,000 contigs with low value of N50 (less than 1000) for Kmer =45. My other assembly for a haploid genome was having 20,000 contigs and N50 around 50,000. Therefore, I'm just wondering how I should improve the velvet assembly in order to improve my assembly. Please may I know if there is any important stuff regarding improving assembly for diploid genome (source where I can get information) , or about any other suitable assembly software for this purpose.
Thank you
Poni
I'm a beginner to the field of sequence analysis.
I'm currently working on assembly of diploid fugal genome which is around the sizes of 60Mb. Sequenced using Illumina HiSeq2000. I have used Velvet assembly software to construct contigs. However, it ended up in more than 100,000 contigs with low value of N50 (less than 1000) for Kmer =45. My other assembly for a haploid genome was having 20,000 contigs and N50 around 50,000. Therefore, I'm just wondering how I should improve the velvet assembly in order to improve my assembly. Please may I know if there is any important stuff regarding improving assembly for diploid genome (source where I can get information) , or about any other suitable assembly software for this purpose.
Thank you
Poni