The NextGENe Pseudo Paired Read Constructor Tool
Paired reads are useful for detection of structural variations such as gene fusion, exon skipping, or read-throughs for transcriptome analysis. The NextGENe Pseudo Paired Read Constructor tool is another tool that you can use to construct paired reads. The NextGENe Pseudo Paired Read Constructor tool creates paired reads from either a reference genome (.fasta file) or sample files. For either file type, the Pseudo Paired Read Constructor tool creates two “paired” reads based on the read length that you specify. You can break the read in half using the entire read or you can specify that the new read length be less than half the original, using only the ends of reads and not the middle. The 5’ end of the read is reversed to form one of the paired reads while 3’ end is used directly as the other read in the pair.
 | To use sample file reads, the reads should be at least 76 bp in length. If original reads are less than 76 bp, you can use the Condensation Tool to increase read length prior to constructing the pseudo paired reads. See Sequence Condensation Tool. |
 | The other option for creating paired reads is the NextGENe Reads Simulator tool. See The NextGENe Reads Simulator Tool. |