I am trying to force AllPaths-LG to use my paired-end data with "standard" insert size of about 300bp.
As per documentation it does fail. But is there a way to fool AllPaths and pass it fragment and jump libraries even though I do not have them?
An idea I had was to run a quick assembly with any assembler (e.g. ABySS) and them map all my reads on it and grab those aligning in a short range and put them in a fragment library file and those aligning at long distance and put them in a jumping library. But I am pretty sure it will fail. Before I try this complicated way, is there any alternative and simpler way to do it?
As per documentation it does fail. But is there a way to fool AllPaths and pass it fragment and jump libraries even though I do not have them?
An idea I had was to run a quick assembly with any assembler (e.g. ABySS) and them map all my reads on it and grab those aligning in a short range and put them in a fragment library file and those aligning at long distance and put them in a jumping library. But I am pretty sure it will fail. Before I try this complicated way, is there any alternative and simpler way to do it?
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