Splice-unaware aligners are able to align continuous reads to a reference genome, but
are not aware of exon/intron junctions. Hence, in RNA-sequencing, splice-unaware
aligners are no proper tool to analyze the expression of known genes, or align reads to
the transcriptome. Splice-aware aligners map reads over exon/intron junctions and are
Fig. 9.4 Smith–Waterman. Optimization of similarity
Fig. 9.5 Smith–Waterman Algorithm and the resulting Scoring Matrix (E). Matches are defined as 2,
Mismatches and Gaps as À1. The traceback is depicted by blue arrows and the corresponding
alignment at the bottom right. Diagonal jumps within the scoring Matrix can be interpreted as
Matches or Mismatches, Top or Down jumps as Deletions, and Left or Right jumps as Insertions
Table 9.1 Splice-aware and splice-unaware alignment tools
Alignment tool
Splice-aware
Link
STAR
Yes
https://github.com/alexdobin/STAR
Bowtie
No
http://bowtie-bio.sourceforge.net/index.shtml
Bowtie2
Yes
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
TopHat/TopHat2
Yes
http://ccb.jhu.edu/software/tophat/index.shtml
BWA-MEM
Yes
http://bio-bwa.sourceforge.net/
BWA-SW
No
BWA-backtrack
No
Hisat2
Yes
https://ccb.jhu.edu/software/hisat2/manual.shtml
Segemehl
Yes
https://www.bioinf.uni-leipzig.de/Software/segemehl/
116
M. Kappelmann-Fenzl