alimg/pforla

Path finding for long read assembly

PForLA - Path Finding for Long read Assembly

This application is designed and developed for CS557 class in Bilkent University.

• To run the application, first you need to generate a DBG with dbgh5 tools provided with gatb-core library. For example;

dbgh5 -in Read1.fq,Read2.fq -kmer-size 19 -out graph -out-dir . -abundance-min 2

• Then, using generated graph, you can run long read path finding by

python3 graph.py <graph.h5> <long_reads.fasta> <output_file.txt> <kmer_size> <use_first_n_reads>

The program will output to stdout; its path coverage and also total length of long read data that it processed.

Found paths will be written in specified output file.