Produces merged raw Illumina paired-end reads with low false positive rates (FPRs). PEAR combines reads by maximizing the assembly score (AS) of the read overlap via a scoring matrix. It evaluates all possible paired-end read overlaps and does not require the target fragment size as input. This method takes quality scores and sequence matches into account.
Offers a merging program. NGmerge rectifies errors and ambiguous bases (Ns) and can be used without the need of a separate adapter-removal step prior to merging reads. This program intends to generate merged reads whose quality scores reflects the most efficiently as possible bases’ error rates. It also includes an alternative mode allowing users to remove contaminating sequencing adapters.