Paired End

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This script takes forward and reverse Illumina reads and joins them using the method chosen. Will optionally create an updated index reads file containing index reads for the surviving joined paired end reads. If the option to write an updated index file is chosen, be sure that the order and header format of the index reads is the same as the order and header format of reads in the files that will be joined (this is the default for reads generated on the Illumina instruments).

SolexaQA calculates sequence quality statistics and creates visual representations of data quality for second-generation sequencing data. Originally developed for the Illumina system (historically known as “Solexa”), SolexaQA now also supports Ion Torrent and 454 data. Running directly on FASTQ files (now with support for compressed files too), the software has three component algorithms: