seqan / flexcat Goto Github PK

This is a fork of seqan_flexbar* which can be found at
https://github.com/seqan/seqan/tree/master/apps/seqan_flexbar

It has been extended and modified in the following ways

- added support for multiple adapters
- added support for 5'-end adapters
- enhanced statistic output of adapter trimming
- added feature to write trimmed sequences to id line
- added feature to write statistics to file
- switched the multithreading design from openMP to std::thread and semaphores
- rewrote most parts of the program, with a generic programming approach

In the future, we plan to integrate flexcat into flexbar.

seqan_flexbar by Sebastian Roskosch is implemented after seqan, 
if you use it, please cite 
[1] Dodt, M.; Roehr, J.T.; Ahmed, R.; Dieterich, "
C.  "FLEXBAR—Flexible Barcode and Adapter Processing for 
Next-Generation Sequencing Platforms. Biology 2012, 1, 895-905.