NOTES

Notes about previous releases

## ImReP 0.3 release 01/04/2017

ImReP 0.3 is available for download here.  This is a new release with the following fixes and changes:

- the -o/ –overlapLen allows to set up the minimal overlap length for reads to be assembled into CDR3 clonotype (second stage of ImReP)
- the -extendedOutput options allows producing two additional files: full_cdr3.txt and partial_cdr3.txt containing detailed information for each read. Details about the format are available at https://github.com/mandricigor/imrep/wiki/ImReP-output
- toy example composed of simulated receptor-derived reads is distributed with the tool. Fasta file with simulated reads is located under example directory

## ImReP 0.2 release 11/30/2016

ImReP 0.2 is available for download here.  This is a new release with the following fixes and changes:

- We have added detailed tutorial available at https://github.com/mandricigor/imrep/wiki
- the -t option has been added to control the stringency of CDR3 clustering.  The value can be from 0.0 to 1.0. Note that thresholds near 1.0 are more liberal and result in more CDR3 to be reported. The default value is 0.2.
- the -c option has been added. Chain types should be separated by comma. The default value is IGH,IGK,IGL,TRA,TRB,TRD,TRG.
- the –noOverlapStep option. This allows to skip the second stage of the ImReP assembly.

## ImReP 0.1 release 11/21/2016

ImReP 0.1 is available for download here. The first public release of ImReP. Because this is the first release, the manual is very limited. Only the basic options have been described, but we plan to update it frequently. If you have any questions about how ImReP works, please contact  Igor Mandric (mandric.igor@gmail.com) and Serghei Mangul (smangul@ucla.edu)