CHESTER

A probabilistic tool to map and visualize relative singularity regions

Introduction

What is CHESTER ?

CHESTER is a probabilistic tool to map and visualize relative singularity regions. The version 1 has been published in RECPAD Conference in October 2015, winning the best poster/paper. Version 2 enables to store data using one bit precision (instead of a byte), automatic setup of Bloom filters, inverted repeats optimization, enlargement of painted (segmented) regions and split of visual from map program. It is a version optimized to cope with large ancient genomes.

It answers the following questions:

How do I get CHESTER ?

Clone our repository and run CMake command:
git clone https://github.com/pratas/chester.git
cd chester/src/
cmake .
make
Alternatively to CMake, run:
git clone https://github.com/pratas/chester.git
cd chester/src/
cp Makefile.nix Makefile
make

Usage

To see the possible options type
./CHESTER-map
or
./CHESTER-map -h
These will print the following options:
Usage: CHESTER-map <OPTIONS>... [FILE]:<...> [FILE]:<...>
CHESTER-map: a tool to map relative singularity regions  
The (probabilistic) Bloom filter is automatically set.

  -v                       verbose mode,
  -a                       about CHESTER,
  -s <value>               bloom size,
  -i                       use inversions,
  -p                       show positions/words,
  -k <value>               k-mer size (up to 30),

  [rFile1]:<rFile2>:<...>  reference file(s),
  [tFile1]:<tFile2>:<...>  target file(s).

The reference files may be FASTA, FASTQ or DNA-SEQ,
while the target files may be FASTA or DNA-SEQ.
Report bugs to <{pratas,ap,pjf}@ua.pt>.
For filtering the content use CHESTER-filter. To see the possible parameters type:
./CHESTER-filter
For visualizing the regions use CHESTER-visual. To see the possible parameters type:
./CHESTER-visual

License

GPL v3 (free for research purposes). For more information see LICENSE file or visit
http://www.gnu.org/licenses/gpl-3.0.html