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2,082 search results found

Soapdenovo2 ⭐ 197

Next generation sequencing reads de novo assembler.

UCSC Genome Browser source tree. Stable branch: "beta".

Nanosim ⭐ 196

Nanopore sequence read simulator

Convolutional neural network analysis for predicting DNA sequence activity.

Doc Annovar ⭐ 193

Documentation for the ANNOVAR software

Circlator ⭐ 193

A tool to circularize genome assemblies

Artemis ⭐ 191

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

Ppanggolin ⭐ 191

Build a partitioned pangenome graph from microbial genomes

dN/dS methods to quantify selection in cancer and somatic evolution

Genome Assembly and Annotation Service code

Chip Seq Pipeline2 ⭐ 188

ENCODE ChIP-seq pipeline

Asciigenome ⭐ 188

Text Only Genome Viewer!

Genvisr ⭐ 188

Genome data visualizations

Full-Length Alternative Isoform analysis of RNA

De novo genome assembler for long uncorrected reads

Methylkit ⭐ 176

R package for DNA methylation analysis

Gtotree ⭐ 174

A user-friendly workflow for phylogenomics

Kubegene ⭐ 169

KubeGene - A turn-key Genome Sequencing workflow management framework

Aligngraph ⭐ 165

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

Tetranscripts ⭐ 164

A package for including transposable elements in differential enrichment analysis of sequencing datasets.

Vgp Assembly ⭐ 160

VGP repository for the genome assembly working group

Genrich ⭐ 158

Detecting sites of genomic enrichment

Insilicoseq ⭐ 158

🚀 A sequencing simulator

Randomly subsample sequencing reads to a specified coverage

Metagem ⭐ 155

💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

Deepevolve ⭐ 151

Rapid hyperparameter discovery for neural nets using genetic algorithms

New Genome Browser (NGB) - a Web - based NGS data viewer with unique Structural Variations (SVs) visualization capabilities, high performance, scalability, and cloud data support

Rust Mdbg ⭐ 149

minimizer-space de Bruijn graphs (mdBG) for whole genome assembly

Metabolic ⭐ 148

A scalable high-throughput metabolic and biogeochemical functional trait profiler

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

Nextpolish ⭐ 145

Fast and accurately polish the genome generated by long reads.

Microassembly based somatic variant caller for NGS data

Layout2im ⭐ 141

Official PyTorch Implementation of Image Generation from Layout - CVPR 2019

Pysamstats ⭐ 141

A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.

Application and Python module for average nucleotide identity analyses of microbes.

Novoplasty ⭐ 140

NOVOPlasty - The organelle assembler and heteroplasmy caller

Bx Python ⭐ 138

Tools for manipulating biological data, particularly multiple sequence alignments

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:

Blobtools ⭐ 136

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets

Mcscanx ⭐ 135

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

Atac_dnase_pipelines ⭐ 135

ATAC-seq and DNase-seq processing pipeline

Genomescope ⭐ 135

Fast genome analysis from unassembled short reads

Genome query language

Hierarchical Alignment Format

Rnaseq Workflow ⭐ 133

A repository for setting up a RNAseq workflow

Openai Neat ⭐ 132

NEAT Solver for OpenAI

Chromosome-level scaffolding using multiple references

Sigprofilerextractor ⭐ 132

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks

Reference Assisted Misassembly Detection Algorithm Using Short and Long Reads

Ngs_learning ⭐ 131

生物信息学交流资料

Winnowmap ⭐ 131

Long read / genome alignment software

Expansionhunter ⭐ 129

A tool for estimating repeat sizes

Viral Ngs ⭐ 129

Viral genomics analysis pipelines

Dna Seq Analysis ⭐ 128

DNA sequencing analysis notes from Ming Tang

Hic_data ⭐ 128

A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.

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.

Assemblytics ⭐ 124

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

Badread ⭐ 124

a long read simulator that can imitate many types of read problems

Genome_updater ⭐ 123

Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

Boosting RNA-Seq assemblies with partial or related genomic sequences

Variantspark ⭐ 121

machine learning for genomic variants

Blacklist ⭐ 121

Application for making ENCODE Blacklists

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

Gena_lm ⭐ 120

GENA-LM is a transformer masked language model trained on human DNA sequence.

Mirdeep2 ⭐ 120

Discovering known and novel miRNAs from small RNA sequencing data

Tensorflow Neuroevolution ⭐ 119

Neuroevolution Framework for Tensorflow 2.x focusing on modularity and high-performance. Preimplements NEAT, DeepNEAT, CoDeepNEAT

Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

Sigminer ⭐ 119

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/

Ampliconarchitect ⭐ 119

AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up so

memote – the genome-scale metabolic model test suite

Carveme ⭐ 117

CarveMe: genome-scale metabolic model reconstruction

Sibeliaz ⭐ 113

A fast whole-genome aligner based on de Bruijn graphs

python access to UCSC genomes database

Px2graph ⭐ 113

Training code for "Pixels to Graphs by Associative Embedding"

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

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

Oncokb Annotator ⭐ 112

Annotates variants in MAF with OncoKB annotation.

Backprop Neat Js ⭐ 112

Neural Network Evolution Playground with Backprop NEAT

Pyrodigal ⭐ 111

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.

Benchmarking Tools ⭐ 110

Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls

Canvas - Copy number variant (CNV) calling from DNA sequencing data

An integrated pipeline for estimating strain-level genomic variation from metagenomic data

Genomic Interactive Visualization Engine ⭐ 108

Genomic Interactive Visualization Engine

Fast HLA type inference from whole-genome data

Vcf Kit ⭐ 107

VCF-kit: Assorted utilities for the variant call format

Genetic Car 2 ⭐ 106

Genetic Cars 2 (Globally Distributed)

Igv Webapp ⭐ 105

Aligngraph2 ⭐ 104

Similar genome assisted reassembly pipeline for PacBio long reads

Pufferfish ⭐ 104

An efficient index for the colored, compacted, de Bruijn graph

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.

Instrain ⭐ 104

Bioinformatics program inStrain

Phandango ⭐ 104

an interactive viewer for populations of bacterial genomes linked by a phylogeny

genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF

Shovill ⭐ 104

⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads

Plyranges ⭐ 103

A grammar of genomic data transformation

Biopieces ⭐ 102

Biopieces is a bioinformatic framework of tools easily used and easily created.

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