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Upfront we need to discuss the two basic assembler types: overlap graph and de Bruijn:
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| src | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928494/figure/F2/ |
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In either case, more and longer reads are better as you can imagine. With an overlap graph (also called overlap layout consensus algorithm or overlap layout algorithm) your assembly grows much more effectively with longer reads and there are few parameters you can tweak. With a de Bruijn approach, obviously your choice of k can have a strong impact on your assembly.
Effect of trade-off in read length and coverage
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| src | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928494/figure/F3/ |
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k-mer distributions inherent in select genomes
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| src | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928494/figure/F1/ |
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Some example assembly statistics
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| src | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928494/table/T1/ |
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Many (many) assemblers are available. A list of assemblers can be found here.
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