Indexing vs Mapping
Hi everyone, I am trying to map some genomes using BBMap. What is indexing a genome? And how does it tie in with mapping? Do you need an indexed genome in order to map? From what I understand it is like building a table of contents for a book so you can find something with ease. What does that mean in terms of mapping sequences? Do you compile a "chapter" (index) of similar sequences?
I'm very new at bioinformatic so a basic explanation would be very helpful! Thank you!
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To Index a genome is to create an index that allows for quick random access to its sequences. See this thread: what is the purpose of indexing a genome
Mapping (to) a genome is the process of mapping (aligning) sequencing reads to a genome. Most aligners will prefer that the genome being aligned to be indexed. Most aligners also have the capability of creating an index if one does not already exist, as indexing is a pretty inexpensive process.