Version:
To compile:
cd <SlopMap HOME>
make
On some machines google hash/map library could not be compiled. In this case, use the following make command:
make stl
This will allow SlopMap use map from the standard library template.
/Usage*******************/
Paired-end Illumina:
./slopmap -1 <PE1 filename> -2 <PE1 filename> -l <Library name> -o <Output prefix> [-k <KMER_SIZE> -d <DISTANCE> -t <THRESHOLD>]
Roche 454:
./slopmap -454 <454 filename> -l <Library name> -o <Output prefix> [-k <KMER_SIZE> -d <DISTANCE> -t <THRESHOLD>]
Default parameters:
-k <KMER_SIZE> 11
-d <DISTANCE> 5 (distance between two consecutive k-mers)
-t <THRESHOLD> 0.75
/Examples*******************/
-Paired-end Illumina:
./slopmap -1 /test_data/R1.fastq.gz -2 /test_data/R2.fastq.gz -o test/test -l test_data/target.fasta
-Roche 454:
./slopmap -454 /test_data/SmallTest.sff -o test -l /test_data/target.fasta -t 0.56 -k 14