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223 search results found

A whole-genome and alignment-free prokaryotic phylogeny tool

Phylonium ⭐ 19

♥ Fast and Accurate Estimation of Evolutionary Distances

Bioinformatics Technology Lab common code library

Linsight ⭐ 19

Necklace ⭐ 19

Combine reference and assembled transcriptomes for RNA-Seq analysis

Vrvizualizer ⭐ 19

A virtual reality visualization system for scientific data.

Topmed_variant_calling ⭐ 18

Aligner for sequencing data

High-level API for storing and querying sequence variant data

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

Nanovar Archived ⭐ 17

Archived version 1.0.2

Maf2synteny ⭐ 17

A tool for recovering synteny blocks from multiple alignment

Svcollector ⭐ 17

Method to optimally select samples for validation and resequencing

Motifmatchr ⭐ 17

Fast motif matching in R

Dupgen_finder ⭐ 17

A pipeline used to identify different modes of duplicated gene pairs

extract MSAs from genome variation graphs

Salmontools ⭐ 16

Useful tools for working with Salmon output

Te_finder ⭐ 16

A suite of C++ programs developed for transposable element search and their annotation in large eukaryotic genome sequence. A part of the REPET package.

Select primer sets for selective whole genome amplification (SWGA)

Disambiguate ⭐ 16

Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem

Metagenomics microbial abundance quantification

Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.

WALT is a read mapping program for bisulfite sequencing DNA methylation studies.

Anno is a variant annotation tool

Pan-genome Seed Index

Genome_painter ⭐ 15

Paint genomes with taxa-specific k-mer probabilities

Informme ⭐ 15

An information-theoretic pipeline for methylation analysis of WGBS data

A streaming method for mapping nanopore raw signals

Bayescenv ⭐ 15

BayeScEnv is a Fst-based, genome-scan method that uses environmental variables to detect local adaptation.

Satsuma2 ⭐ 14

FFT cross-correlation based synteny aligner, (re)designed to make full use of parallel computing

ABLE - Approximate Blockwise Likelihood Estimation

Debruijn ⭐ 14

de Bruijn graph construction tool

profile basd Illumina pair-end Reads Simulator

Mutatrix ⭐ 14

genome simulation across a population with zeta-distributed allele frequency, snps, insertions, deletions, and multi-nucleotide polymorphisms

Allele-Specific Quantification of Structural Variations in Cancer Genomes

Accucopy ⭐ 13

Accucopy is a computational method that infers Allele-specific Copy Number alterations from low-coverage low-purity tumor sequencing Data.

Minhash Index Extended to Knead Kmer Intersection

Metaothello ⭐ 13

Ritornello ⭐ 13

Ritornello is a high fidelity control free ChIP-seq peak calling algorithm

Metaphase ⭐ 12

The software involved in the MetaPhase project, as described in G3 (http://dx.doi.org/10.1534/g3.114.011825)

A Sliding Window Approach to Identify Differentially Methylated Regions Based on Whole Genome Bisulfite Sequencing

Pyseqarray ⭐ 12

PySeqArray: data manipulation of whole-genome sequencing variants with SeqArray files in Python (pre-release version)

Readserver ⭐ 12

Using reference-free compressed data structures to analyse thousands of human genomes (1000 Genomes ReadServer)

Virhostmatcher Net ⭐ 12

VirHostMatcher-Net: A network-based computational tool for predicting virus-host interactions.

Haploconduct ⭐ 11

Haplotype-aware genome assembly toolkit

Mscaffolder ⭐ 11

A comparative genome scaffolding tool

Cnefinder ⭐ 11

CNEFinder: Finding Conserved Non-coding Elements in Genomes

SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity

Strainest ⭐ 11

StrainEst - abundance estimation of strains

De-novo Assembly Structural Variant Caller

Relative Fm ⭐ 11

Relative data structures based on the BWT

Hotspot2 ⭐ 10

Implementation of hotspot2 by Eric Rynes

Fast Bayesian Hidden Markov Model with Wavelet Compression

Ttree Source ⭐ 10

Exploiting SNP correlations within Random Forest for Genome-Wide Association Studies

FMtree: A fast locating algorithm of FM-indexes for genomic data

Gencode Backmap ⭐ 10

Mapping of GENCODE gene annotation set files to older assembies

A clone of the official AMOS git repo on sourceforge: https://sourceforge.net/projects/amos/

Demographic inference from whole genomes

De novo genome assembler.

A bioinformatics tool for SV detection and virus integration discovery

Parallel String Graph Construction, Transitive Reduction, and Contig Generation for De Novo Genome Assembly

De Bruijn graph construction for large k.

Ppa Assembler ⭐ 9

A toolkit for de novo genome assembly based on Pregel.

Source code for SimBac, a bacterial genome simulator

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

High-speed and high-ratio referential genome compression

Spydrpick ⭐ 9

SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.

Jackalope ⭐ 8

A swift, versatile phylogenomic and high-throughput sequencing simulator

Nucleotide PanGenome explorer

Bayesian variable selection and model averaging in genome-wide association analysis

Easygwascore ⭐ 8

Computational Framework for Genome-Wide Association Studies and Meta-Studies in C/C++ with Python Interfaces

Sparseassembler ⭐ 8

A sparse k-mer graph based, memory-efficient genome assembler.

fast classification of metagenomic sequences with lightweight de Bruijin graph-based reference indexing

robust matching of small variant datasets using flexible scoring schemes

Ssimp_software ⭐ 7

acdc - (a)utomated (c)ontamination (d)etection and (c)onfidence estimation for single-cell genome data

Trace intervals between genomes using a synteny map

i-ADHoRe is a highly sensitive software tool to detect degenerated homology relations within and between different genomes.

Ascertained Sequentially Markovian Coalescent

Hicaptools ⭐ 7

A software suite for Probe Design and Proximity Detection for targeted chromosome conformation capture applications

MeTaxa: an advanced taxonomy classifier for unknown genomic and metagenomic sequences

A tool that evolves small brains capable of scanning and classifying an image.

MIML-DML : Multi-Instance Multi-Label Distance Metric Learning for Genome-Wide Protein Function Prediction

Cuda Neat ⭐ 6

Parallel evaluation of NEAT genomes.

Selection ⭐ 6

Rapid linking of long reads to a reference genome

This repository contains code of ALGA - short read de novo genome assembler.

Disty McMatrixface - compute a distance matrix from a core genome alignment file

Hgt Finder ⭐ 6

Program for finding horizontal gene transfer using BLAST result

conserved non-coding sequence

Dashing Experiments ⭐ 6

Experiments for the Dashing manuscript

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