isovic

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Croatia, Singapore

http://www.sovic.org/

Ivan Sovic's starred repositories

awesome-modern-cpp

A collection of resources on modern C++

Language:HTML11606 492 20

bioconda-recipes

Conda recipes for the bioconda channel.

Language:ShellMIT1599 95 1873

vg

tools for working with genome variation graphs

Language:C++NOASSERTION1085 48 2022

GenomeWorks

SDK for GPU accelerated genome assembly and analysis

Language:CudaApache-2.0278 18 219

MashMap

A fast approximate aligner for long DNA sequences

Language:C++NOASSERTION260 17 47

GraphAligner

Language:C++MIT253 15 96

pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.

BSD-3-Clause-Clear243 29 683

racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads

Language:C++MIT195 12 60

pbmm2

A minimap2 frontend for PacBio native data formats

Language:PerlBSD-3-Clause-Clear166 200

hts-nim

nim wrapper for htslib for parsing genomics data files

Language:NimMIT154 10 55

ksw2

Global alignment and alignment extension

Language:CNOASSERTION127 14 23

BandageNG

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

Language:C++GPL-3.0110 11 90

FASTK

A fast K-mer counter for high-fidelity shotgun datasets

Language:CNOASSERTION110 11 22

Peregrine

Peregrine: Fast Genome Assembler Using SHIMMER Index

Language:Jupyter NotebookNOASSERTION99 8 35

pyliftover

Pure-python implementation of UCSC liftOver genome coordinate conversion

Language:PythonMIT87 6 17

astarix

AStarix: Fast and Optimal Sequence-to-Graph Aligner

Language:C++MPL-2.072 11 5

FALCON-Phase

FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds

Language:CNOASSERTION72 10 59

Minipolish

A tool for Racon polishing of miniasm assemblies

Language:PythonGPL-3.071 8 11

graphmap2

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1

Language:C++MIT65 5 24

HINGE

Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution"

Language:C++NOASSERTION64 14 85

libgaba

Adaptive semi-global banded alignment on string graphs

Language:C63 6 11

kxsort

Fast in-place radix sort with STL-like API

Language:C++44 4 2

FALCON_unzip

Making diploid assembly becomes common practice for genomic study

Language:PythonBSD-3-Clause-Clear30 25 159

pbipa

Improved Phased Assembler

BSD-3-Clause-Clear26 100

ra

This repository is deprecated, please use the link to the right.

Language:PythonMIT23 5 12

pbbam

PacBio BAM C++ library

Language:C++BSD-3-Clause-Clear21 150

rala

Layout module for raw de novo genome assembly of long uncorrected reads.

Language:C++MIT21 5 3

adaptivebandbench

Benchmark on adaptive banded algorithm

Language:C18 4 2

automation-panda-resources

Resources for Automation Panda, my blog about software testing and career anecdotes

DASCRUBBER-wrapper

Wrapper script for easier read scrubbing with DASCRUBBER

Language:PythonGPL-3.01000