1. A nucleic acid sequencing system for compressing sequencing data, comprising: a) a processor; and b) a memory coupled with the processor and having instructions that when executed by the processor perform a method comprising: i) receiving a collection of data strings corresponding to a first set of nucleotide data for a first nucleic acid fragment being sequenced in the system; ii) identifying a first character representing a first nucleotide in each of the data strings in the collection; iii) generating a first Burrows Wheeler transform index for a compressed data string containing the first characters corresponding to a first nucleotide of each data string; iv) identifying an additional character representing an additional nucleotide in each of the data strings; and v) updating the first Burrows Wheeler transform index with the additional characters corresponding to each additional nucleotide of the received collection of data strings to form compressed sequencing data.