ICC is a software pipeline to analyze next-generation sequencing data (454 pyrosequencing, Ion Torrent, etc.), including read quality filtering and alignment, indel and carryforward error correction, single nucleotide variant calling, and calculation of nucleotide variant and hyplotype frequencies. ICC was written in Perl scripting language and has been tested on Linux, Mac OS X and MS Windows systems. The most recent version is ICC_v2.0.

ICC source code and example data:

• ICC_v2.0

  - Release date: June 20, 2014.

  - ICC can be run in parallel, which allows users to define number of processors to run ICC based on their computing resource and dramatically reduces the running time.



• ICC_v1.2

  - Release date: May 6, 2014.

  - Adds an option in runICC.pl to assemble reads from continuous windows before and after ICC (please note that, if there is overlap or gap between windows, the assembling will not perform appropriately).



• ICC_v1.1

  - Release date: Oct 29, 2013.

  - Fixes the bug that may cause incorrect clustering in IC step if consensus is not the most frequent sequence in a cluster in HIC step.

  - Fixes the bug that outputs warning messages in calculating nucleotide frequencies if there is only one sequence after error correction.



• ICC_v1.0

  - Initial release: July 29, 2013.

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