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Search results for c plus plus genomics

70 search results found

tools for working with genome variation graphs

Nucleus ⭐ 675

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

Bwa Mem2 ⭐ 645

The next version of bwa-mem

A high-performance, Pythonic language for bioinformatics

Bowtie2 ⭐ 594

A fast and sensitive gapped read aligner

Hifiasm ⭐ 443

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Megahit ⭐ 442

Ultra-fast and memory-efficient (meta-)genome assembler

Oxford Nanopore's Basecaller

Octopus ⭐ 285

Bayesian haplotype-based mutation calling

Haplotype VCF comparison tools

🔬 BEDOPS: high-performance genomic feature operations

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

Chromap ⭐ 166

Fast alignment and preprocessing of chromatin profiles

Genomicsqlite ⭐ 146

Genomics Extension for SQLite

Cgranges ⭐ 144

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

Blacklist ⭐ 121

Application for making ENCODE Blacklists

Sibeliaz ⭐ 113

A fast whole-genome aligner based on de Bruijn graphs

Kmer Cnt ⭐ 106

Code examples of fast and simple k-mer counters for tutorial purposes

Assembly Stats ⭐ 92

Get assembly statistics from FASTA and FASTQ files

Bwa Meme ⭐ 92

BWA-MEME: Faster BWA-MEM2 using learned-index

Genomicsdb ⭐ 88

High performance data storage for importing, querying and transforming variants.

Wally: Visualization of aligned sequencing reads and contigs

Tiledb Vcf ⭐ 79

Efficient variant-call data storage and retrieval library using the TileDB storage library.

Fast hash function for DNA/RNA sequences

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

Estimating k-mer coverage histogram of genomics data

Gatb Core ⭐ 61

Core library of the Genome Analysis Toolbox with de-Bruijn graph

Pax_sapientica ⭐ 61

🌿: GIS for philological, archaeological, and anthropological data.

A secure encryption tool for genomic data

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

vcfdist: Accurately benchmarking phased variant calls

Functional genomics and genome-wide association studies

Kmerstream ⭐ 46

Streaming algorithm for computing kmer statistics for massive genomics datasets

A versatile compressor of third generation sequencing reads.

A fast constructor of the compressed de Bruijn graph from many genomes

A fast tool for hybrid genome assembly of long and short reads

Gfakluge ⭐ 36

A C++ library and utilities for manipulating the Graphical Fragment Assembly format.

Mindthegap ⭐ 30

MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.

Optimized sequence graph implementations for graph genomics

Split Kmer Analysis

Segalign ⭐ 26

A Scalable GPU-Based Whole Genome Aligner, published in SC20: https://doi.ieeecomputersociety.org/10.1109/SC4140

Forward-time simulation in Python using fwdpp

simple viewer for variant call format using htslib

Qtip: a tandem simulation approach for accurately predicting read alignment mapping qualities

Phage-Host Interaction Search Tool

Command-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format

High-level API for storing and querying sequence variant data

Metabcc Lr ⭐ 16

Reference-free Binning of Metagenomics Long Reads using Coverage and Composition

A long-read analysis toolbox for cancer and population genomics

SAPLING: Suffix Array Piecewise Linear INdex for Genomics

Linear-time, low-memory construction of variation graphs

Fastq compression

Ultrafast sequence typing and gene detection from NGS raw reads

TeraPCA is a multithreaded C++ software suite based on Intel's MKL library (or any other BLAS and/or LAPACK distribution). TeraPCA features no dependencies to external libraries and combines the robustness of subspace iteration with the power of randomization.

A universal genomic coordinate translator for comparative genomics

BreakID: genomics breakpoints identification to detect gene fusion events using discordant pairs and split read

Fast Bayesian Hidden Markov Model with Wavelet Compression

SOPanG, a simple tool for pattern matching over an elastic-degenerate string, a recently proposed simplified model for the pan-genome.

🌈Alignment-free scaffolding of genome assemblies with 10x Genomics Chromium reads

Kmercamel ⭐ 9

KmerCamel🐫 provides implementations of several algorithms for efficiently representing a set of k-mers as a masked superstring.

Lightweight C++ library for reading FASTA and FASTQ files.

a C++ API of htslib to be easily integrated and safely used. More importantly, it can be callled seamlessly in R/Python/Julia etc.

fast and comprehensive k-mer counting package

Kmer Counter ⭐ 8

Count kmers with a more efficient (faster) hash table

MOI and Allele Frequency Recovery from Noisy Polyallelic Genetics Data

Smart and Accurate Polishing of Phase Haplotypes Integrating Read Enhancements (SAPPHIRE)

Genome Browser ⭐ 6

Genome browser to visualize and analyze genomic data

Cutevariant Cpp ⭐ 6

a gui tools to filtering genomics variation

Streaming de Bruijn and Compact de Bruijn Graph Algorithms

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