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77 search results found

tools for working with genome variation graphs

Diamond ⭐ 900

Accelerated BLAST compatible local sequence aligner.

Nucleus ⭐ 675

Python and C++ code for reading and writing genomics data.

Jellyfish ⭐ 419

A fast multi-threaded k-mer counter

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads

UGENE is free open-source cross-platform bioinformatics software

Aligngraph ⭐ 165

Algorithm for secondary de novo genome assembly guided by closely related references

breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R.

Boosting RNA-Seq assemblies with partial or related genomic sequences

Regtools ⭐ 103

Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.

Image vectorizer throught evolution

Metagraph ⭐ 81

Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly

A fast 23andMe DNA parser and inferrer for Python

Fm Index ⭐ 71

FM-Index full-text index implementation using RRR Wavelet trees (libcds) and fast suffix sorting (libdivsufsort) including experimental results.

Methpipe ⭐ 63

A pipeline for analyzing DNA methylation data from bisulfite sequencing.

Nanocall ⭐ 61

An Oxford Nanopore Basecaller

COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)

G-BLASTN is a GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST.

Find and visualize rearrangements in DNA sequences

Bioinfortools ⭐ 42

Bioinformatics scripts and tools

Cosmo is a fast, low-memory DNA assembler using a Succinct (variable order) de Bruijn Graph.

Batmeth2 ⭐ 36

BS-seq analysis pipeline

Antonie is an integrated, robust, reliable and fast processor of DNA reads

Libpandadna ⭐ 36

A parser for Disney's DNA files. It focus primarily on Toontown's DNA.

Fast FASTA/Q parser and writer (C++ re-implementation of kseq library)

Paired Tag ⭐ 33

Analysis of Paired-Tag datasets

A new version of the code to simulate the oxDNA/oxRNA models, now equipped with Python bindings

Split Kmer Analysis

DNA, Amino Acid and RNA Tests

Holosqape ⭐ 24

Qt and QML based Holochain container app

Aoapc Uva Answer ⭐ 21

算法竞赛入门经典例题和习题答案刘汝佳第二版

Gargammel ⭐ 20

gargammel is an ancient DNA simulator

Hi-C Interaction Frequency Inference (HIFI): High-resolution estimation of DNA-DNA interaction frequency from Hi-C data

Physis Shard ⭐ 18

Artificial Intelligence Library

Gmicromc ⭐ 17

Bayesian reconstruction of ancient DNA fragments

Schmutzi ⭐ 16

Maximum a posteriori estimate of contamination for ancient samples

Biocpp Core ⭐ 16

BioC++ core library (alphabet, meta, ranges)

Structural Variation and fusion detection using targeted sequencing data from circulating cell free DNA

Overlapping Reads COmpression with Minimizers

Dna_rs_coding ⭐ 14

Error correction scheme for storing information on DNA using Reed Solomon codes

GAGA is a fast, header only, multi-objective, and distributed evolutionary algorithm library written in modern C++. It is designed to be easily usable with various genotype representations and allows the user to enable or disable several features such as novelty search or speciation. It also produces and exports various customizable statistics.

FaStore - high-performance FASTQ files compressor

Dnastore ⭐ 12

Software for error-tolerant coding of information into DNA sequences using finite-state transducers.

Ultrafast sequence typing and gene detection from NGS raw reads

Bha_thermocycler ⭐ 12

Thermocycler for PCR

High-performance stochastic modeling of DNA loop extrusion interactions

Description Extractor ⭐ 11

HGVS variant description extractor

Dungeon Crawl Stone Soup: Circus Animals fork

Programmable keyboard software for Windows

Srassembler ⭐ 9

Selective and Recursive local Assembler

PgRC: Pseudogenome based Read Compressor

Methimpute ⭐ 8

Impute DNA methylation from WGBS data.

Planet Evo ⭐ 8

evolution simulation software

A boost library for genetic searches

Biotechnology protocols improved with Artificial Intelligence for the MIT biotechnology tournament, and more. Check out our website!

Probabilities for Pedigrees Given DNA Data

opencl image evolver

Masa Core ⭐ 6

Multi-Platform Architecture for Sequence Aligner (MASA) is a flexible software framework that simplifies the creation of DNA sequence alignment applications in multiple hardware/software platforms. This framework is based on CUDAlign and it supports huge DNA sequences with more than 200 million base pairs.

Fast tool for sequence related tasks

Monsterlab ⭐ 6

Monster Lab: teaching the science of sequencing with Lego

牛客网题解

HEDGES Error Correcting Code for DNA

Peng Motif ⭐ 5

PEnG-motif is an open-source software package for searching statistically overrepresented motifs (position specific weight matrices, PWMs) in a set of DNA sequences.

A graph-based genotyper for aligned DNA sequencing data

This repo contains leetcode question solutions . I try to add solutions of as many solutions as I can .

Dna Compression ⭐ 5

A simple example which shows how DNA data can be efficiently stored in C++.

Cleancall ⭐ 5

Correction for DNA contamination in genotype calling

A comprehensive, accurate and efficient solution for analysis of large scale base-resolution DNA methylation data

A parallel DNA k-mer counter based on optimized distributed memory hash tables

Pufferfish ⭐ 5

Super simple, super lightweight dna compression tool

Using C and C++ code from R

Jellyfish ⭐ 5

Fork of the jellyfish kmer counter. Here is the description copied from their site: JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting th

Syzygy Tools ⭐ 5

A collection of tools to help developers of SYZYGY carriers and peripherals

A simple yet powerful sequence clustering tool.

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