FLASH v1.2.10 (Identifies paired-end reads which overlap in the middle, converting them to single long reads)
FLASH, Fast Length Adjustment of SHort reads, is a very accurate fast tool to merge paired-end reads from fragments that are shorter than twice the length of reads. The extended length of reads has a significant positive impact on improvement of genome assemblies.
Merging mate pairs by FLASH as a pre-processor for genome assembly yields singificantly higher N50 value of contigs and scaffolds. It also reduces the number of missassembled contigs.