Reference-guided cDNA assembly using related genomes

ohofmann · 02-08-2011, 10:20 AM

Dear all,

taken a look through the forum to find related questions. While there are plenty of tools for reference guided RNA-seq assembly (TopHat/Cufflinks, etc.) in general is there anything that can use the genome of a related species (at, say, 90% sequence similarity level) to guide the assembly process?

I could obviously tweak the alignment step and pass these on to an assembler, or go with a de novo assembler, just want to make sure I'm not overlooking an existing solution.

Cheers, Oliver

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02-08-2011, 10:20 AM	#1
ohofmann Member Location: Melbourne, Australia Join Date: Jan 2009 Posts: 37	Reference-guided cDNA assembly using related genomes Dear all, taken a look through the forum to find related questions. While there are plenty of tools for reference guided RNA-seq assembly (TopHat/Cufflinks, etc.) in general is there anything that can use the genome of a related species (at, say, 90% sequence similarity level) to guide the assembly process? I could obviously tweak the alignment step and pass these on to an assembler, or go with a de novo assembler, just want to make sure I'm not overlooking an existing solution. Cheers, Oliver