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Result file name — file in SAM format to write the result of the alignment into. This parameter is required.
Library - single-end or paired-end reads.
Prebuilt index — check this box to use an index file instead of a source reference sequence. The index is a set of 6 files with suffixes .1.ebwt, .2.ebwt, .3.ebwt, .4.ebwt, .rev.1.ebwt, and .rev.2.ebwt. The index is created during the alignment. Also you can build it manually.
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You can also configure other parameters. They are the same as in the original Bowtie 2 (you can read detailed description of the parameters on the Bowtie 2 manual page).
Select one of the following alignment modes:
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