Paired end reads are provided as a single read containing the pair joined by a linker sequence. When assembling 454 paired end reads, SeqMan NGen will check for the presence of a linker defining the paired end reads. Reads with an identifiable linker are split into forward and reverse reads with the forward read flipped so the traditional orientation is maintained. These reads are then put into parallel fastq files. SeqMan NGen appends each file name with _1 or _2, following the Illumina paired end convention. The read names themselves are appended with __for or __rev. In cases where the linker occurs at the end of the read, the linker is removed and a single end read is placed in a file with _unpaired appended to the name. Reads where no read is detected are also placed in the _unpaired file. 454 paired end splitting can also be specified through scripting.