PygenoPersonalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
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AioliFramework for building fast genomics web tools with WebAssembly and WebWorkers
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Vcfannoannotate a VCF with other VCFs/BEDs/tabixed files
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QqmanAn R package for creating Q-Q and manhattan plots from GWAS results
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Eggnog MapperFast genome-wide functional annotation through orthology assignment
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Quota AlignmentGuided synteny alignment between duplicated genomes (within specified quota constraint)
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BioBioinformatics library for .NET
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gff3toemblConverts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
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Jigvigv.js server and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"
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GenomeAnalysisModuleWelcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.
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Kmer CntCode examples of fast and simple k-mer counters for tutorial purposes
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bacnetBACNET is a Java based platform to develop website for multi-omics analysis
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RadiatorRADseq Data Exploration, Manipulation and Visualization using R
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dna-traitsA fast 23andMe genome text file parser, now superseded by arv
Stars: ✭ 64 (-51.15%)
DkmDynamic Kernel Matching (DKM) for Classifying Data with Non-conforming Features
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tiptoftPredict plasmids from uncorrected long read data
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BwaBurrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
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mcscanCommand-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format
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CgrangesA C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)
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MAGMA CelltypingFind causal cell-types underlying complex trait genetics
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Awesome 10x GenomicsList of tools and resources related to the 10x Genomics GEMCode/Chromium system
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awesome-geneticsA curated list of awesome bioinformatics software.
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Tiledb VcfEfficient variant-call data storage and retrieval library using the TileDB storage library.
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chromapFast alignment and preprocessing of chromatin profiles
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Somalierfast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
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plasmidtronAssembling the cause of phenotypes and genotypes from NGS data
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BgdataA Suite of Packages for Analysis of Big Genomic Data
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SvtyperBayesian genotyper for structural variants
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FALDOFeature Annotation Location Description Ontology
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Vgtools for working with genome variation graphs
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smartas📓Notebook of Climente-González et al. (2017), The Functional Impact of Alternative Splicing in Cancer.
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MsprimeSimulate genealogical trees and genomic sequence data using population genetic models
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staramrScans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
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NucleusPython and C++ code for reading and writing genomics data.
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calN50Compute N50/NG50 and auN/auNG
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Fastq.bioAn interactive web tool for quality control of DNA sequencing data
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catchA package for designing compact and comprehensive capture probe sets.
Stars: ✭ 55 (-58.02%)
DeeptoolsTools to process and analyze deep sequencing data.
Stars: ✭ 448 (+241.98%)
saffrontreeSaffronTree: Reference free rapid phylogenetic tree construction from raw read data
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HicexplorerHiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
Stars: ✭ 116 (-11.45%)
echtvarecht rapid variant annotation and filtering
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GoatoolsPython library to handle Gene Ontology (GO) terms
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GubbinsRapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
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wdlRunRElastic, reproducible, and reusable genomic data science tools from R backed by cloud resources
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Bwa Mem2The next version of bwa-mem
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perfPERF is an Exhaustive Repeat Finder
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SmudgeplotInference of ploidy and heterozygosity structure using whole genome sequencing data
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JbrowseA modern genome browser built with JavaScript and HTML5.
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Benchmarking ToolsRepository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
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SarekDetect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
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NglessNGLess: NGS with less work
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AribaAntimicrobial Resistance Identification By Assembly
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Dna NnModel and predict short DNA sequence features with neural networks
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JvarkitJava utilities for Bioinformatics
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