Hi Folks,
I am using Velvet to assemble a number of genes where the reads are of 75bp length. An issue I am having is that some of these genes are a result of duplications, where the parent and duplicate gene are very similar. Am I right in thinking that a high k-mer length will reduce that chances of an assembly error (smaller k-mers being merged as one contig despite coming from reads generated from duplicates). I realize sequencing errors may be unavoidable, hopefully good coverage will help avoid these. If longer k-mers are better for duplicates would it be better to generate longer reads?
I am using Velvet to assemble a number of genes where the reads are of 75bp length. An issue I am having is that some of these genes are a result of duplications, where the parent and duplicate gene are very similar. Am I right in thinking that a high k-mer length will reduce that chances of an assembly error (smaller k-mers being merged as one contig despite coming from reads generated from duplicates). I realize sequencing errors may be unavoidable, hopefully good coverage will help avoid these. If longer k-mers are better for duplicates would it be better to generate longer reads?
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