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and so if this is clear we can go into how this sequence gets represented for the computer to understand the the standard format for these sequences is fast cube and it looks something like this when youamp;#39;re working with this you will receive files with millions and millions of reads of lines in each direction but one read is going to look more or less like this here you have two reads each one has four lines and the second line of the read is going to be the DNA sequence that the sequencer identified then the fourth line is going to be the quality of that sequence so quality is usually encoded as Fred plus 33 which goes from 0 to 41 the highest quality bases are going to be at the beginning which you see here is like the second highest quality and then the quality starts decreasing at the end with like different characters Fred fred is just a scoring system for translating the probability of being a mistake the higher the more certain we are of the base of the read of the nucle
