Clone the project

git clone --recursive https://github.com/Malfoy/pyranha.git

Compile the project: compile the mapping tool

cd pyranha
./install.sh

Example commandline for the mapping tool:

/!\ Warning : all fasta files sequences must be written on one line.

• 1- Perform kmer counting with KMC:

  ./scripts/kmerCount.py data/1Mrna.fa data/smallref.fa 15 data/smallref15mer

• 2- Map reads on reference:

  ./bin/kIWImap -u data/1Mrna.fa -x data/smallref.fa -b data/smallref15mer -k 15 -t 8

Example Output

Filling index of data/smallref.fa

Indexing took : 0 sec

Mapping data/1Mrna.fa

Reads: 1000000

Reads mapped: 403638

Percent Read mapped: 40.3638%

Reads not mapped: 596362

Mapping took : 7 sec

Throughout: 142k read by second or 514M by hour

Example command line for the de novo discovery tool: ./bin/kIWI ./tools/kIWI_denovo/test/test.fa result.out

Example Output ping-pong: AACGTGCCAT +: 0, 1, -: 2, 3,

The first line means ping pong has been found in the data with a 10-mer overlap "AACGTGCCAT", the reads participating are reads 0 and 1 of the dataset for the + strand, 2 and 3 for the - strand.