Short Read Vs Long Read

Since the Illumina/Pacbio deal was announced I've had a quite a few folks ask me to explain the difference between short read (Illumina) and long read (PacBio) sequencing. This analogy seems to help: imagine two versions of the same jigsaw puzzle, one with 10 pieces and the other with 1,000 pieces. Putting together the 10 piece puzzle is easy, you don't even need to look at the picture on the box, you can just fit the pieces together by looking at their shapes. But putting together the 1,000 puzzle is impossible unless you look at the original picture. Long read is like the 10 piece puzzle, you have nice long sequences and you can put them together without looking at anything else. Short read is like the 1,000 piece puzzle - you need an existing sequence to provide the clues you need to assemble the new sequence. So if short read sequencing is harder to assemble, why did Illumina win this battle? Simple: Illumina puzzles are about ten times cheaper than PacBio puzzles - and people want to do a lot of puzzles.