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Search results for c plus plus bioinformatics
bioinformatics
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c-plus-plus
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129 search results found
Nucleus
⭐
675
Python and C++ code for reading and writing genomics data.
Salmon
⭐
661
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
Bwa Mem2
⭐
645
The next version of bwa-mem
Vsearch
⭐
605
Versatile open-source tool for microbiome analysis
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
Hh Suite
⭐
429
Remote protein homology detection suite.
Raxml Ng
⭐
339
RAxML Next Generation: faster, easier-to-use and more flexible
Manta
⭐
333
Structural variant and indel caller for mapped sequencing data
Survivor
⭐
299
Toolset for SV simulation, comparison and filtering
Avogadro
⭐
283
Avogadro 1 is not under active development, the repository was archived in September 2021. Development of Avogadro 2 is being done at https://github.com/openchemistry/avogadrolibs. Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
Hap.py
⭐
283
Haplotype VCF comparison tools
Abyss
⭐
276
🔬 Assemble large genomes using short reads
Sortmerna
⭐
250
SortMeRNA: next-generation sequence filtering and alignment tool
Bedops
⭐
244
🔬 BEDOPS: high-performance genomic feature operations
Strelka
⭐
204
Strelka2 germline and somatic small variant caller
Krakenuniq
⭐
201
🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
Ugene
⭐
190
UGENE is free open-source cross-platform bioinformatics software
Chromap
⭐
166
Fast alignment and preprocessing of chromatin profiles
Graphtyper
⭐
156
Population-scale genotyping using pangenome graphs
Cgranges
⭐
144
A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)
Poplddecay
⭐
138
PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
Spoa
⭐
135
SIMD partial order alignment tool/library
Muscle
⭐
134
Multiple sequence alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.
Rnaseqc
⭐
132
Fast, efficient RNA-Seq metrics for quality control and process optimization
Blacklist
⭐
121
Application for making ENCODE Blacklists
Strobealign
⭐
114
Aligns short reads using dynamic seed size with strobemers
Sibeliaz
⭐
113
A fast whole-genome aligner based on de Bruijn graphs
Swarm
⭐
110
A robust and fast clustering method for amplicon-based studies
Physicell
⭐
107
PhysiCell: Scientist end users should use latest release! Developers please fork the development branch and submit PRs to the dev branch. Thanks!
Phyx
⭐
100
phylogenetics tools for linux (and other mostly posix compliant) computers
Msisensor
⭐
99
microsatellite instability detection using tumor only or paired tumor-normal data
Bwa Meme
⭐
92
BWA-MEME: Faster BWA-MEM2 using learned-index
Assembly Stats
⭐
92
Get assembly statistics from FASTA and FASTQ files
Gramtools
⭐
90
Genome inference from a population reference graph
Genomicsdb
⭐
88
High performance data storage for importing, querying and transforming variants.
Arcs
⭐
86
🌈Scaffold genome sequence assemblies using linked or long read sequencing data
Tiledb Vcf
⭐
79
Efficient variant-call data storage and retrieval library using the TileDB storage library.
Arv
⭐
75
A fast 23andMe DNA parser and inferrer for Python
Cafe
⭐
71
Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
Kmer Db
⭐
68
Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).
Bonsai
⭐
68
Bonsai: Fast, flexible taxonomic analysis and classification
Gatb Core
⭐
61
Core library of the Genome Analysis Toolbox with de-Bruijn graph
Fastv
⭐
56
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.
Gbwt
⭐
55
Substring index for paths in a graph
Metabuli
⭐
54
Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.
Cogaps
⭐
53
Bayesian MCMC matrix factorization algorithm
Gblastn
⭐
52
G-BLASTN is a GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST.
Cath Tools
⭐
51
Protein structure comparison tools such as SSAP and SNAP
Metacache
⭐
49
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
Vcfdist
⭐
48
vcfdist: Accurately benchmarking phased variant calls
Bioinfortools
⭐
42
Bioinformatics scripts and tools
Haslr
⭐
39
A fast tool for hybrid genome assembly of long and short reads
Twopaco
⭐
39
A fast constructor of the compressed de Bruijn graph from many genomes
Pyalign
⭐
38
Fast and Versatile Alignments for Python
Shapeit5
⭐
38
Segmented HAPlotype Estimation and Imputation Tool
Megadock
⭐
38
An ultra-high-performance protein-protein docking for heterogeneous supercomputers
Covtobed
⭐
36
⛰ covtobed | Convert the coverage track from a BAM file into a BED file
Rkmh
⭐
32
Classify sequencing reads using MinHash.
Gclib
⭐
30
GCLib - Genomic C++ library of reusable code for bioinformatics projects
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.
Fastenloc
⭐
28
Colocalization analysis of genetic association signals
Pandoras Toolbox For Bioinformatics
⭐
26
A collection of well-known bioinformatics programs.
Goldrush
⭐
26
Linear-time de novo Long Read Assembler
Snapr
⭐
25
SNAPR: a bioinformatics pipeline for efficient and accurate RNA-seq alignment and analysis
Meshclust
⭐
25
MeShClust: an intelligent tool for clustering DNA sequences
Sina
⭐
24
SINA - Reference based multiple sequence alignment
Hibag
⭐
23
R package – HLA Genotype Imputation with Attribute Bagging (development version only)
Snpsea
⭐
23
📊 Identify cell types and pathways affected by genetic risk loci.
Qtip
⭐
23
Qtip: a tandem simulation approach for accurately predicting read alignment mapping qualities
Cutevcf
⭐
23
simple viewer for variant call format using htslib
Genamap
⭐
22
Visual Machine Learning of Genome-Phenome Associations
Phist
⭐
22
Phage-Host Interaction Search Tool
Haploclique
⭐
21
Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.
Compairr
⭐
20
Comparison of Adaptive Immune Receptor Repertoires
Phylonium
⭐
19
♥ Fast and Accurate Estimation of Evolutionary Distances
Btllib
⭐
19
Bioinformatics Technology Lab common code library
Gengis
⭐
18
GenGIS (pronounced 'Genghis' like Genghis Khan) is a bioinformatics application that allows users to combine digital map data with information about biological sequences collected from the environment. GenGIS provides a 3D graphical interface in which the user can navigate and explore the data, as well as a Python interface that allows easy scripting of statistical analyses using the Rpy libraries.
Ultra
⭐
18
ULTRA Locates Tandemly Repetitive Areas
Ckmeans.1d.dp
⭐
18
❗ This is a read-only mirror of the CRAN R package Ckmeans.1d.dp — Optimal, Fast, and Reproducible Un
Fasql
⭐
18
DuckDB Extension for reading and writing FASTA and FASTQ Files
Svcollector
⭐
17
Method to optimally select samples for validation and resequencing
Plink2
⭐
17
pLink is a software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry.
Motifmatchr
⭐
17
Fast motif matching in R
Pyascore
⭐
16
A python package for fast post translational modification localization, powered by Cython.
Lorax
⭐
16
A long-read analysis toolbox for cancer and population genomics
Vargeno
⭐
15
Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.
Setriq
⭐
14
Fast string distance computation in Python
Physiboss
⭐
14
Multiscale simulation of multi-cellular system
Taxor
⭐
13
Fast and space-efficient taxonomic classification of long reads
Fast Simple Lcsk
⭐
13
Fast and simple algorithms for computing both LCSk and LCSk+
Lib310
⭐
13
lib310 python package
Cbioinfcpp 0
⭐
12
The lib CBioInfCpp.h contains 3 groups of functions for C++: "Input-Output", "Working with strings", "Working with graphs". Data structures "Adjacency vector" and "Adjacency map" are implemented in the last one (i.e. in "Working with graphs"). See About_CBioInfCpp for details.
Pyseqarray
⭐
12
PySeqArray: data manipulation of whole-genome sequencing variants with SeqArray files in Python (pre-release version)
Modle
⭐
12
High-performance stochastic modeling of DNA loop extrusion interactions
Terapca
⭐
12
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.
Meshclust2
⭐
11
MeShClust2: Application of alignment-free identity scores in clustering long DNA sequences
Scinsight
⭐
11
Matrix factorization model for interpreting single cell gene expression in biologically heterogeneous data
Guidescan Cli
⭐
10
A gRNA database generation tool.
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