Sahara

Approximate searches using Optimum Search Schemes

Usage

1. Create an index for a fasta file:

    $ sahara index somefastafile.fasta

2. Search inside the index and allow 2 errors accordingly to edit distance:

    $ sahara search --index somefastafile.fasta.idx --query queryfile.fasta --errors 2

Compile from Source

To compile the source, download it through git and build it with cmake/make. At the end we execute the help page.

git clone https://github.com/seqan/sahara.git
mkdir -p sahara/build && cd $_
cmake -DCMAKE_BUILD_TYPE=Release ..
make
./src/sahara/sahara --help