- MAQ
- BowTie, BWA, Soap2 (uses Burrows–Wheeler Transform [38], a
technique previously used for compression) The
BWT string is built by sorting all of the circular
shifts of a string, and concatenating the last characters
of each circular shift 'last-first property'
- mrFAST
pair reads are useful for large structural variations (insertions, deletions, translocations), problem with inserts that are larger than the expected distance between pairs (try hanging-reads - only of the reads are mapped)
ABI Solid's colorspace is useful for SNP analysis
This approach also
demonstrates a key advantage of the color-space
encoding. When one compares a regular, letter-
space read to a known DNA sequence, it is difficult
to determine if a discrepancy is due to a true differ-
ence between the two genomes, or to a sequencing
error. In color-space, we can usually separate the two
explanations: if the difference is due to an SNP
between the genomes, this will lead to two adjacent
color-space changes, as both of the colors that inter-
rogated the nucleotide will change.
On the other hand, a sequencing error will only
affect one color, and therefore can be differentiated
from a SNP.
color-space Smith-Waterman - aligns the reference of all 4 possible translations (like transcript to protein)
problem with repeats, non-uniform coverage
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