Example:
9.2.3.2 Bowtie
Bowtie is an ultrafast and memory-efficient short read alignment tool to large reference
genomes indexed with a Burrows–Wheeler index. It is typically used for aligning DNA
sequences as it is a splice-unaware tool. Because of this feature this tool is often used in
microbiome alignment (http://bowtie-bio.sourceforge.net/index.shtml) [11, 12].
9.2.3.3 Bowtie2
Bowtie2, as well as Bowtie, is an ultrafast and memory-efficient tool, but more suitable for
aligning sequencing reads of about 50 up to 100s or 1,000s of characters to relatively long
reference sequences (e.g., mammalian genomes) indexed with an Ferragina–Manzini (Fm)
index. Bowtie2 supports gapped, local, and paired-end alignment modes (https://github.
com/BenLangmead/bowtie2) [13].
118
M. Kappelmann-Fenzl
9.2.3.2 Bowtie
Bowtie is an ultrafast and memory-efficient short read alignment tool to large reference
genomes indexed with a Burrows–Wheeler index. It is typically used for aligning DNA
sequences as it is a splice-unaware tool. Because of this feature this tool is often used in
microbiome alignment (http://bowtie-bio.sourceforge.net/index.shtml) [11, 12].
9.2.3.3 Bowtie2
Bowtie2, as well as Bowtie, is an ultrafast and memory-efficient tool, but more suitable for
aligning sequencing reads of about 50 up to 100s or 1,000s of characters to relatively long
reference sequences (e.g., mammalian genomes) indexed with an Ferragina–Manzini (Fm)
index. Bowtie2 supports gapped, local, and paired-end alignment modes (https://github.
com/BenLangmead/bowtie2) [13].
118
M. Kappelmann-Fenzl