New feature! Gap patching using long reads

For bacterial-sized genomes, ALLPATHS-LG now accepts an additional data type as input: long reads (for example from Pacific Biosciences), and uses these reads to patch gaps in scaffolds obtained from short reads.  We recommend using high coverage (e.g. 25-100x) by long reads because they have a high error rate.  Typically, all small gaps in scaffolds disappear.  Note that the standard short read libraries (from fragments and jumps) are still required.

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