The <font color="red"><u>C</u></font>ache <font color="red"><u>AS</u></font>sisted <font color="red"><u>H</u></font>ash Search with <font color="red"><u>X</u></font>or logic (<font color="red">CASHX</font>) Pipeline can be used to parse, map, quantify and manage large quantities of short-read sequence data. CASHX is a set of tools that can be used together, or as independent modules on their own. The reference genome alignment tools can be used with any reference sequence in fasta format. The pipeline was designed and tested using Arabidopsis thaliana small RNA reads generated using an Illumina 1G. Currently there is no size limit to the query sequence allowing it to be used for short and long read data. Also the method under witch the database is constructed increases accuracy without the cost of speed. The CASHX Pipeline was created by the Jim Carrington Lab at Oregon State University.
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