snegl

SNEGL is a free software tool to compute maximal exact matches (MEMs) between two dna or protein sequences. It can be used in a pipeline for the computation of alignments based on a seed-and-extend approach. SNEGL is based on an extension of the free software library SDSL (see https://github.com/simongog/sdsl-lite/). The needed clone of the SDSL can be found here (https://github.com/dorleosterode/sdsl-lite/tree/dna_optimized_wt).

SNEGL can also compute maximal unique matches (MUMs) and super-maximal exact matches (SMEMs), which can be used as seeds as well or as representation of MEMs.

The directory bwa contains a test-programm for the computation of SMEMs. It depends on the BWA library (see https://github.com/lh3/bwa).

Requirments and Dependencies

snegl depends on a fork of the sdsl-lite library (see: https://github.com/simongog/sdsl-lite, the fork in the right branch can be found here: https://github.com/dorleosterode/sdsl-lite/tree/dna_optimized_wt), so you have to install it. You can follow the install instructions given in the README. To use snegl you further have to fulfill the following requirements:

• A modern, C++11 ready compiler such as g++ version 4.7 or higher or clang version 3.2 or higher.

snegl is only tested on 64-bit Linux-systems, but you can try to use it on different architectures.

The test-programm BWA-SMEM depends on the BWA library (see: https://github.com/lh3/bwa). To use the test-programm you have to install BWA using the install instructions in the README.

BWA-SMEM is also tested only on 64-bit Linux-systems.

Download and Compilation

You can download snegl with the following command.

git clone https://github.com/dorleosterode/snegl.git

To compile snegl use:

make SDSL_DIR=/path/to/sdsl

The variable SDSL_DIR contains the absolute path to the directory, where the sdsl-lite is installed. The default value for SDSL_DIR is /usr/bin. If you have installed the sdsl-lite library there you can just use:

make

If you need a static linked version of snegl use:

make static

You can remove the executable and all object-files with:

make clean

To compile BWA-SMEM use:

cd bwa
make BWA_DIR=/path/to/bwa

You can remove BWA-SMEM and all object-files with:

make clean

Getting started

To compute the MEMs of minimal length 20 for a reference Sequenz REF.fa and a query sequence QUERY.fa in the FASTA format use the following command:

./snegl -l 20 REF.fa QUERY.fa

The results are written to a file called "output.sdsl.out". You can change the filename with the parameter -o. So calling:

./snegl -l 20 -o new_output.txt REF.fa QUERY.fa

will write the results in the file "new_output.txt".

You can compute MUMs for the same setting as before with:

./snegl -l 20 --mum REF.fa QUERY.fa

and SMEMs with:

./snegl -l 20 --smem REF.fa QUERY.fa

respectivly. For other options see:

./snegl --help