kd-tree-overlapper

Fast and memory-efficient noisy read overlapping with KD-trees.

Software licensed under the Apache License 2.0, using the FLANN and SeqAN software libraries (and including klib's kseq.h to parse FASTA/FASTQ input). Please see INSTALL.md for instructions how to install kd.

Usage:

./kd [options] -i <input_file>

Options:
     -o outputfile with overlaps [overlaps.out]
     -k length of k-mers for geometric embedding [4]
     -r number of iterations for ANN search [600]
     -l length of tags (subreads placed on reads) [1200]
     -s average distance between tags [600]
     -n number of ANNs per tag, [40]
     -m minimum allowed distange between tags [200]
     -w window size for GC-peaks detection [100]
     -v prints version and quit
     -i input FASTA file