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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.

aligneval

Framework for evaluating third and second generation sequencing alignments.

aracon

Assembly with RApid CONsensus from raw noisy long reads

argparser

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

bandage

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

bioconda-recipes

Conda recipes for the bioconda channel.

c3pu

C3PU is a 16-bit soft-core processor implemented in VHDL using Xilinx ISE Webpack.

cgmemtime

cgmemtime measures the high-water RSS+CACHE memory usage of a process and its descendant processes.

cigargen

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

consensus_from_mpileup

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

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.

evalue

E-value calculation with predefined BLAST parameters.

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

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:

graphmap-reproduce

Scripts for testing and validating GraphMap.

graphmap-server

hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

isovic.github.io

isres

isRes is a simple Python script for measuring resource consumption on Linux platforms.

leftalign

Python scripts to left align indels in SAM files.

marginalign

UCSC Nanopore

minialign

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

notes

Log of useful commands, tips and tricks.