Decode a FASTQ before you trust it
Explain the four FASTQ lines and why quality scores shape every downstream choice.
The move: read the file contract before reading the biology. A FASTQ read has four parts: identifier, sequence, plus line, and quality string. The sequence tells you what bases were called. The quality string tells you how confident the instrument was at each position. The key beginner mistake is treating FASTQ as just "a file of DNA letters." It is really DNA letters plus evidence about uncertainty. The mechanism is simple: every later tool assumes the input is structured. A trimmer uses quality scores to decide whether to trim ends. An aligner may use qualities when scoring mismatches. A variant…
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