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Assemble Independently

This mode works in exactly the same way as normal shotgun assembly (see section Normal Shotgun Assembly) with all its options and settings, except that the new batch of data is assembled independently of all the data already in the database. This means that the only overlaps found will be between the readings in the current batch. One role for this mode would be to assemble a batch of data that was known from the way it was produced (say a set of nested clones covering some problem region such as a repeat) to overlap. Use of Assemble Independently will ensure that the batch of readings will only be overlapped with one another, and will not be aligned with other similar regions of the consensus. Once assembled in this way they can be joined to other contigs using Find Internal Joins.See section Find Internal Joins.


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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_18.html