CASHX Pipeline

The Cache ASsisted Hash Search with Xor logic (CASHX) Pipeline can be used to parse, map, quantify and manage large quantities of 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.

 

Pipeline Downloads

Current Production Release Date Download
Release 2.3 10/15/2010 CASHX.tar.gz

 

All Current Releases Date Download
Release 2.3 10/15/2010 CASHX_2.3.tar.gz
Release 2.2 06/14/2010 CASHX_2.2.tar.gz
Release 2.1 03/09/2010 CASHX_2.1.tar.gz
Release 2.0 (Beta) 03/11/2009 CASHX_2.0.tar.gz
Release 1.3 02/17/2009 CASHX_1.3.tar.gz
Release 1.2 01/16/2009 CASHX_1.2.tar.gz

 

Release Information and Known Problems

  • Release 2.3 - SAM complaint output
  • Release 2.2 - Work with paired end data
  • Release 2.1 - Allows for mismatch bases, throttle hits, best hits, unique hits and memory control. This version will format genomes larger than 3GBases
  • Release 2.0 - Formatting of genomes larger than 500M base may require 16G bytes memory or more
  • Release 1.x - Limit of 500M base for reference genome size

Publications of CASHX

Fahlgren N., Sullivan, C.M., Kasschau, K.D., Chapman, E.J., Cumbie, J.S., Montgomery, T.A., Gilbert, S.D., Dasenko, M., Backman T.W., Givan, S.A., Carrington, J.C. (2009) Computational and analytical framework for small RNA profiling by high-throughput sequencing. RNA 15, 992-1002.

 

Help and Bug Reports

Please submit questions or bug reports here.