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There are two main types of assembly - denovo and mapped - with the latter not really being a true assembly at all.

Denovo assembly consists of an assembly of DNA fragments without typically knowing any of the goal target sequence. Hence it compares sequence fragments against each other in order to form contigs. Mapped assembly makes uses of a known reference sequence and compares all sequence fragments against the reference, which is a far simpler and faster process than denovo assembly.

Gap5 however has neither denovo or mapped assembly built-in. Instead it relies on externally running standard command-line tools. At present this consists purely of using bwa for a mapped assembly, but in future this will be expanded upon.

This means that the Assembly menu currently only contains a "Map Reads" sub-menu, which is turn has multiple choices for bwa usage. You will not be directly able to join contigs using these facilities or to fill holes in the contig, although this is possible by manually following some of the steps outlined below and using an alternate step for generating the SAM file.


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Last generated on 25 November 2011.