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Does bowtie2 align sequences longer than reference sequences? #2

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pieterprovoost opened this issue Jan 12, 2023 · 0 comments

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pieterprovoost commented Jan 12, 2023

The docs are not entirely clear:

Bowtie 2 is geared toward aligning relatively short sequencing reads to long genomes. That said, it handles arbitrarily small reference sequences (e.g. amplicons) and very long reads (i.e. upwards of 10s or 100s of kilobases), though it is slower in those settings. It is optimized for the read lengths and error modes yielded by typical Illumina sequencers.

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