Ivan Sovic

racon. Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:

graphmap. GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:

raptor. Graph-based mapping of long sequences, noisy or HiFi.

wavelet-image-compression. Simple FPGA-based Wavelet Image Compression

aligned_vector. An STL-like std::vector implementation which internally aligns the array to a desired number of bytes. Intended for e.g. SIMD purposes.

minialign. Minimalistic aligner which uses Minimap for input mapping locations and Edlib for fast bitvector alignment.

cigargen. Simple DP implementation of Needleman-Wunsch for generating CIGAR strings for sequence alignments.

aracon. Assembly with RApid CONsensus from raw noisy long reads

consensus_from_mpileup. Scripts to compute simple consensus (SNPs, insertions, deletions) from mpileup by majority vote.

marginAlign. UCSC Nanopore

samscripts. Python

seqlib. A codebase for sequence analysis projects. Highly experimental and in development.

graphmap-reproduce. Scripts for testing and validating GraphMap.

argparser. Library for parsing command line arguments. Allows short and long arg names, specifying parameter groups and default values.

evalue. E-value calculation with predefined BLAST parameters.