Hi!
I have three Ion torrent libraries; a 600bp, 400bp and a 200bp library. I intend to use SPAdes to assemble the reads into contigs but am unsure whether I can use three different sized libraries in a single assembly? (As I'm pretty sure it's going to have an affect on the optimal k-mer value).
Has anyone used various read sizes in a single assembly or would it be wiser to assemble one library at a time and use the resultant contigs from the first assembly as "untrusted contigs" in the next assembly and so on?
Any advice would be massively appreciated!!
I have three Ion torrent libraries; a 600bp, 400bp and a 200bp library. I intend to use SPAdes to assemble the reads into contigs but am unsure whether I can use three different sized libraries in a single assembly? (As I'm pretty sure it's going to have an affect on the optimal k-mer value).
Has anyone used various read sizes in a single assembly or would it be wiser to assemble one library at a time and use the resultant contigs from the first assembly as "untrusted contigs" in the next assembly and so on?
Any advice would be massively appreciated!!
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