AgilePairedEndReadsCombiner
Combining paired end read data sequences to form a single extended read.
AgilePairedEndReadsCombiner reads a matching pair of fasta or fastq files created from a paired end sequence run which used PCR products as the library template and combines the data to produce a single read file contain data equivalent to the whole PCR product.
When comparatively short PCR products are sequenced to produce paired end reads the entire length of the PCR amplicon may be sequenced, but data is present in two different files. AgilePairedEndReadsCombiner is able to read matched paired sequence data files and identify the region of overlap between two reads from the same molecule and then combine them to form a single read. If the data is in fastq files, then the quality strings are also combined. If a position present in both reads and is different in each read, the position is given the value of the base with the highest quality score. For positions common to both reads the highest quality score is retained in the exported quality string.
It is possible to set the minimum and maximum size range of the sequenced products and set the number of combined reads saved to each combined read file.
Guide to use of AgilePairedEndReadsCombiner :
The AgilePairedEndReadsCombiner user guide can be found here.
Download
The AgilePairedEndReadsCombiner program can be downloaded here.