Ivan Sovic's repositories
hifiasm
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
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:
bioconda-recipes
Conda recipes for the bioconda channel.
DALIGNER
Find all significant local alignments between reads
gindex
A gapped-spaced index with minimizer support.
FALCON-Phase
FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds
leftalign
Python scripts to left align indels in SAM files.
Bandage
a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
fork
Subset of pitchfork
DAMASKER
Module to determine where repeats are and make soft-masks of said
aligneval
Framework for evaluating third and second generation sequencing alignments.
sam2json
Overlapper evaluation from read-to-reference alignment
emptyproject
An empty template makefile project.
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.
notes
Log of useful commands, tips and tricks.
gotoh
An implementation of the Gotoh alignment algorithm.
daemon
A template for a threaded file monitoring daemon.
simdhmm
This is a toy project aiming at implementing a SIMD accelerated Hidden Markov Model framework.
edlib
C/C++ library for sequence alignment using edit distance based on Myers's "Fast Bit-Vector Algorithm for Approximate String Matching Based on Dynamic Programming"
graphmap-reproduce
Scripts for testing and validating GraphMap.