processing mate-pair data from Illumina's nextera protocol.
Inspired by nextclip.
to build simply type
on any unix system
requires that zlib be installed on your system. Optionally you can also read from bzip2 formatted files by typing
prepmate will output five files in gzip format. Two for each of the mate-pair and paired-end reads produced during processing and a singletons files.
There is also a log file describing the alignments of the adaptor sequence to the reads and there eventual fate in the dataset.