isovic

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.

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.

aracon

Assembly with RApid CONsensus from raw noisy long reads

samscripts

argparser

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

graphmap-reproduce

Scripts for testing and validating GraphMap.

seqlib

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

aligneval

Framework for evaluating third and second generation sequencing alignments.

Bandage

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

bioconda-recipes

Conda recipes for the bioconda channel.

daemon

A template for a threaded file monitoring daemon.

DALIGNER

Find all significant local alignments between reads

DAMASKER

Module to determine where repeats are and make soft-masks of said

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"

emptyproject

An empty template makefile project.

FALCON-Phase

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

fork

Subset of pitchfork

gindex

A gapped-spaced index with minimizer support.

gotoh

An implementation of the Gotoh alignment algorithm.

graphmap-server

hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

isovic.github.io

leftalign

Python scripts to left align indels in SAM files.

notes

Log of useful commands, tips and tricks.

sam2json

Overlapper evaluation from read-to-reference alignment

simdhmm

This is a toy project aiming at implementing a SIMD accelerated Hidden Markov Model framework.

Sparc