9.2.3.6 HISAT2
HISAT (and its newer version HISAT2) is the next generation of spliced aligner from the
same group that has developed TopHat. HISAT uses an indexing scheme based on the
Burrows–Wheeler transform and the Ferragina–Manzini (Fm) index, employing two types
of indices for alignment: a whole-genome Fm index to anchor each alignment and
numerous local Fm indexes for very rapid extensions of these alignments (https://github.
com/DaehwanKimLab/hisat) [15].
HISAT most interesting features include its high speed and its low memory requirement.
HISAT is an open-source software freely available. A detailed description of the usage of
HISAT can be found in the HISAT manual (https://ccb.jhu.edu/software/hisat2/manual.
shtml).
Take Home Message
• Sequence alignment is the process of comparing and detecting distances/
similarities between biological sequences.
• Dynamic programming technique can be applied to global alignments by using
methods such as global and local alignment algorithms.
• The value that measures the degree of sequence similarity is called the alignment
score.
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M. Kappelmann-Fenzl