Modified by wym6912

SplitMEM can be used on Windows and Linux platforms.

Make programs

Linux

cd src && make THREADS=16

Usage:

./SplitMEM
        Usage: ./SplitMEM [options]

Available options:
        --inputfile/-i    FILE  input file name (required)
        --outputfile/-o   FILE  output file name (required)
        --kmer/-k         k     K-mer size (required)
        --method/-m             use method to construct SA {SAIS, DIV, PARDIV} (default: DIV)
        --threads/-t      t     use t threads to construct SA (only effected in PARDIV)
        --nocache/-n            do not use cache in program
        --help/-h               print help message
        --version/-v            print program version
Sample usage: ./SplitMEM -i 1.fasta -k 10 -o 1.ans

Contact:

• wym6912 [email protected]

RAW README

Graphical pan-genome analysis with compressed suffix trees and the Burrows-Wheeler transform Uwe Baier Timo Beller Enno Ohlebusch

Algorithm: These are the algorithms proposed in Graphical pan-genome analysis with compressed suffix trees and the Burrows-Wheeler transform Submitted to BIOINF-2015-1242 Please cite the paper above, if you use one of theses algorithms.

Requirements: - a modern c++11 ready compiler such as gcc version 4.7 - the Succinct Data Structure Library (sdsl-lite) (version d533b2600950b4f878cb063ca0cd1bf340c53df4, maybe newer)

Install:

1. Install the SDSL by the commands:

git clone [email protected]:simongog/sdsl-lite.git sdsl-lite
cd sdsl-lite
./install.sh [PATH]

2. Save the path of the sdsl into the variable SDSLLITE e.g. by:

export SDSLLITE=[PATH to SDSL]

3. Build the executables by the command:

make

cst_based: Has theoretical running time $O(n)$.

Example: ./cst_based.x 10 input.fa output

with

10       = k
input.fa = the input file in FASTA
output   = the output filename

Will produce the file output file containing the de Bruijn graph.

bwt_based: Has theoretical running time $O(n \log \sigma)$ but in practice fast than cst_based. The space requirement is roughly 1.5n Byte + size of the compressed de Bruijn graph.

Example: ./bwt_based.x input.fa example kfile.txt

with

input.fa = the input file in FASTA
example  = the output filename
kfile.txt= a file containing the values of k

Will produce two files for each $k$ in kfile.txt:

example.k*k*.dot
example.k*k*.start_nodes.txt

Where the *.dot files contain the de Bruijn graph and the *.start_nodes.txt contains the list of the start nodes.

Notes: The programs should compile with commit d533b2600950b4f878cb063ca0cd1bf340c53df4, of the SDSL, but may also work with newer versions of the SDSL.

Limitations: The input file must be in FASTA format, especially the input may not contain the 0-byte or 1-byte, newlines and characters between '>' and the next newline will be removed. k must be smaller than the shortest sequence.