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Search results for c plus plus genome

223 search results found

tools for working with genome variation graphs

A single molecule sequence assembler for genomes large and small.

Bowtie2 ⭐ 594

A fast and sensitive gapped read aligner

Nanopolish ⭐ 496

Signal-level algorithms for MinION data

Hifiasm ⭐ 443

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Megahit ⭐ 442

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

Unicycler ⭐ 428

hybrid assembly pipeline for bacterial genomes

Vcftools ⭐ 415

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

Graph-based alignment (Hierarchical Graph FM index)

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

Fastani ⭐ 301

Fast Whole-Genome Similarity (ANI) Estimation

Multineat ⭐ 289

Portable NeuroEvolution Library

Haplotype VCF comparison tools

🔬 Assemble large genomes using short reads

Mashmap ⭐ 243

A fast approximate aligner for long DNA sequences

Augustus ⭐ 237

Genome annotation with AUGUSTUS

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

Centrifuge ⭐ 215

Classifier for metagenomic sequences

Genome-wide Efficient Mixed Model Association

Krakenuniq ⭐ 201

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

De novo genome assembler for long uncorrected reads

Aligngraph ⭐ 165

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

Regenie ⭐ 148

regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.

Dashing ⭐ 147

Fast and accurate genomic distances using HyperLogLog

Graphmap ⭐ 137

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms113 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:

Mcscanx ⭐ 135

MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!

Hierarchical Alignment Format

Reference Assisted Misassembly Detection Algorithm Using Short and Long Reads

Expansionhunter ⭐ 129

A tool for estimating repeat sizes

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

Blacklist ⭐ 121

Application for making ENCODE Blacklists

Sibeliaz ⭐ 113

A fast whole-genome aligner based on de Bruijn graphs

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data

Fast HLA type inference from whole-genome data

Aligngraph2 ⭐ 104

Similar genome assisted reassembly pipeline for PacBio long reads

Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.

SKESA assembler

Pan-genome inference and genotyping with long noisy or short accurate reads

MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads

Clonalframeml ⭐ 92

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

🌈Scaffold genome sequence assemblies using linked or long read sequencing data

Spliced read mapper for RNA-Seq

Opera Ms ⭐ 82

OPERA-MS - Hybrid Metagenomic Assembler

An R package for performing STAAR procedure in whole-genome sequencing studies

A fast 23andMe DNA parser and inferrer for Python

Genome mapping and spliced alignment of cDNA or amino acid sequences

Bonsai: Fast, flexible taxonomic analysis and classification

Minia is a short-read assembler based on a de Bruijn graph

Cuttlefish ⭐ 64

Building the compacted de Bruijn graph efficiently from references or reads.

Ray -- Parallel genome assemblies for parallel DNA sequencing

GenMap - Fast and Exact Computation of Genome Mappability

The genome assembler that reduces the computational time of human genome assembly from 400,000 CPU hours to 2,000 CPU hours, utilizing long erroneous 3GS sequencing reads and short accurate NGS sequencing reads.

An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.

Genome comparison via de Bruijn graph. To get the latest stable version, please visit our site.

Liftover ⭐ 51

liftover for python, made fast with cython

reference-guided aligner for next-generation sequencing technologies

Metacache ⭐ 49

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

Functional genomics and genome-wide association studies

W2rap Contigger ⭐ 44

An Illumina PE genome contig assembler, can handle large (17Gbp) complex (hexaploid) genomes.

A program to call variants from genome alignment

piRNA pipeline collection developed in the Zamore Lab and ZLab in UMass Med School

Seqarray ⭐ 41

Data management of large-scale whole-genome sequence variant calls (Development version only)

A coalescent simulator for genome-scale sequences

Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop

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

Isaac_variant_caller ⭐ 38

This project is deprecated, please see strelka2 at https://github.com/Illumina/strelka

Isaac_aligner ⭐ 38

Isaac Genome Alignment Software

Fast spliced aligner with low memory requirements

This toolkit deals with GEnomic sequence and genome structure ANnotation files between inbreeding lines and species.

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

Batmeth2 ⭐ 36

BS-seq analysis pipeline

Ltr_finder ⭐ 35

LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences.

Smartie Sv ⭐ 34

calling SVs from Blasr contig level alignments

Classify sequencing reads using MinHash.

In-silico PCR, primer design and padlock design for in-situ sequencing

Population-wide Deletion Calling

Popcogent ⭐ 30

Microbial Populations as Clusters Of Gene Transfer

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.

Gotcloud ⭐ 29

Genomes on the Cloud, Mapping & Variant Calling Pipelines

Minemonics ⭐ 29

(Alpha Stage, work in progress) An open-source 3D virtual creature evolution simulator built in OGRE rendering engine in C++ to experiment with emergent gait-periodicity in evolved creatures on unknown terrain.

Enhanced Artificial Genome Engine: next generation sequencing reads simulator

Argweaver ⭐ 28

Sampling and manipulating genome-wide ancestral recombination graphs (ARGs)

Population Reference Graphs for the HLA and MHC.

Population-scale detection of novel sequence insertions

Pandoras Toolbox For Bioinformatics ⭐ 26

A collection of well-known bioinformatics programs.

Segalign ⭐ 26

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

ChIP-seq DC and QC Pipeline

Fastq Scan ⭐ 24

Output FASTQ summary statistics in JSON format

Blastfrost ⭐ 23

A fast and memory-efficient k-mer counter with GPU-support

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

Biokanga ⭐ 22

An integrated high performance bioinformatics toolkit

Identification of segmental duplications in the genome

Visual Machine Learning of Genome-Phenome Associations

HyPo: Super Fast & Accurate Polisher for Long Read Genome Assemblies

Automated human exome/genome variants detection from FASTQ files

k-SLAM ultra fast alignment and taxonomic classification of metagenomic datasets

Aligner for sequencing data

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