This software is the implementation of egsa [1,4] (http://link.springer.com/chapter/10.1007%2F978-3-642-38905-4_20), an external memory algorithm to construct generalized enhanced suffix arrays.

Given a collection of K strings, egsa outputs the:

• Generalized suffix array
• LCP-array
• Burrows-Wheeler transform.

git clone https://github.com/felipelouza/egsa.git
cd egsa

Compile

make compile 

Given a collection of K strings concatenated in a single file INPUT in the directory DIR.

fasta

make run DIR=dataset/fasta/ INPUT=proteins-100.fasta K=100

fastq

make run DIR=dataset/fastq/ INPUT=reads-100.fastq K=100

txt

make run DIR=dataset/txt/	INPUT=input-100.txt K=100

• strings are separated per '\0' (new line)

Examples

One could find examples in dataset folder, at least one for each setting mode.

The generalized enhanced suffix array is stored in the same directory DIR in a file called:

$(INPUT).K.gesa

Temporary files are stored in folders

$(DIR)/partition/
$(DIR)/tmp/

Output the Burrows-Wheeler transform:

make compile BWT=1

One can inform the maximum available internal memory to be used (in MB):

make clean
make compile MEMLIMIT=10

debug

To see a more detailed execution output use:

make compile DEBUG=1

One can check if the output produced by egsa is correct:

make run CHECK=1

##external resources:

We have included the source codes of the following algorithms:

• gsaca-k: generalized suffix array construction algorithm [2]
• lcp-PHI: LCP-array construction algorithm given the suffix array [3]

Please, if you use egsa tool in an academic setting cite the following paper:

@article{Louza2017d,
	author = {Louza, Felipe A. and Telles, Guilherme P. and Hoffmann, Steve and Ciferri, Cristina D. A.},
	title={Generalized enhanced suffix array construction in external memory},
	journal={Algorithms for Molecular Biology},
	year = {2017},
	pages = {26:1--26:16},
	doi = {10.1186/s13015-017-0117-9}
}

[1] Louza, F. A., Telles, G. P., Ciferri, C. D. A. (2013). External Memory Generalized Suffix and LCP Arrays Construction. In Proc. CPM (pp. 201-210).

[2] Louza, F. A., Gog, S., Telles, G. P. (2016). Induced Suffix Sorting for String Collections. In Proc. DCC (pp. 43-52), https://github.com/felipelouza/gsa-is

[3] Kärkkäinen, J., Manzini, G., & Puglisi, S. J. (2009). Permuted Longest-Common-Prefix Array. In G. Kucherov & E. Ukkonen (Eds.), Proc. CPM (Vol. 5577, pp. 181–192).

[4] Louza, F. A., Telles, G. P., Hoffman, S., Ciferri, C. D. A. (2017). Generalized enhanced suffix array construction in external memory, Algorithms for Molecular Biology.

##thanks:

Thanks to Fabio Garofalo, Giovanna Rosone and Guilherme P. Telles by helpful suggestions and debugging.