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Like an index for a book (in the olden days before Kindles and Nooks), creating an index for a computer database allows quick access to any "record" given a short "key". In the case of mapping programs, creating an index for a reference sequence allows it to more rapidly place a read on that sequence at a location where it knows at least a piece of the read matches perfectly or with only a few mismatches. By jumping right to these spots in the genome, rather than trying to fully align the read to every place in the genome, it saves a ton of time.

Indexing is a separate step in running most mapping programs because it can take a LONG time if you are indexing a very large genome (like our own overly complicated human genome). Furthermore, you only need to index a genome sequence once, no matter how many samples you want to map. Keeping it as a separate step means that you can skip it later when you want to align a new sample to the same reference sequence.

This command can take a while (~5 minutes) and is extremely taxing. This is longer than we want to run a job on the head node (especially when all of us are doing it at once). In fact, in previous years, TACC has noticed the spike in usage when multiple students forgot to make sure they were on idev nodes and complained pretty forcefully to us about it. Let's not have this be one of those years. Use the showq -u command to make sure you are on an idev node. If you are not sure if you are on an idev node, speak up on zoom and I'll show(q) -u what you are looking for. Yes, your instructor likes bad puns. My apologies.

If you are not on an idev node, and need help to relaunch it, click over to the idev tutorial.