What should be the standard output of a mapper (not aligner)?
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6.3 years ago
manetsus ▴ 40

As far I know, a mapper is an intermediary state of reads of a genome where the reads are clustered in a special format. It just makes the task of aligner easier.

Often aligner is also called mapper, but mapper should not be used as an alternative of aligner.

Do I have any wrong concept about mapper?

However, what information must exist in the output of a mapper?

Say, AFIK, aligner gives output in an standard format called sam file, where the fields are standardized.

Does there exist any such kind of file format in case of mapper? If no, then what should be the standard fields (columns) of a mapper?

Please provide some names of mapping tools which give outputs either in the same format or in different formats.

Note that, I ran minimap which is one of the mapping tool.

mapper genome • 1.4k views
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You would find this thread interesting: Alignment and mapping

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Yes, I also felt that after reading several papers that terms mappers and aligners are used alternatively, but now-a-days, they are different. However, I am trying to work with long reads. So, mapper should be different here. Thanks for the link.


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