The CASHX Pipeline
The Cache ASsisted Hash Search with Xor logic (CASHX) 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.
Pipeline Downloads
| Current Production Release | Date | Download |
|---|---|---|
| Release 1.3 | 02-17-2009 | CASHX.tar.gz |
| All Current Releases | Date | Download |
|---|---|---|
| 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 |
Known Problems
- 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.
Publication 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, in press.
Help and Bug Reports
Please send question or bug reports to: cashx@cgrb.oregonstate.edu