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Considerations when designing DNA sequencing software

I am about to start working on a project where I will support programmers develop software for:

a) Alignment of reads against a genomic reference

b) De-novo sequence assembly

Can anyone provide general advice on software design strategies to consider? This is specifically with regard to variations in read lengths and error rates between different sequencing techniques.

sequencing alignment software error
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updated by Biostar Biostar • written by pauldavism • pauldavism

The general strategy is to not reinvent the wheel. There are a LOT of aligners and assemblers already around, so the question becomes (A) why they feel the need to write yet another one and (B) if they've looked at what other programs are doing. Have a look at what BWA is doing, since it can handle a few different kinds of sequencing technologies (bbmap too, since it seems to support everything).

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written by Devon Ryan Devon Ryan

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