Abstract: Polynucleotide sequencing generates multiple reads of a polynucleotide molecule. Many or all of the reads may contain errors. Trace reconstruction takes multiple reads generated by a polynucleotide sequencer and uses those multiple reads to reconstruct accurately the nucleotide sequence. The types of errors are substitutions, deletions, and insertions. The location of an error in a read is identified by comparing the sequence of the read to the other reads. The type of error is determined by comparing both the base call of the read at the error location and base calls of the read and other reads in a look-ahead window that includes base calls adjacent to the error location. A consensus output sequence is developed from the sequences of the multiple reads and identification of the error types for errors in the reads.