MixomicsDevelopment repository for the Bioconductor package 'mixOmics '
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tiptoftPredict plasmids from uncorrected long read data
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Vgtools for working with genome variation graphs
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mcscanCommand-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format
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SvtyperBayesian genotyper for structural variants
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MAGMA CelltypingFind causal cell-types underlying complex trait genetics
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NucleusPython and C++ code for reading and writing genomics data.
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AioliFramework for building fast genomics web tools with WebAssembly and WebWorkers
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awesome-geneticsA curated list of awesome bioinformatics software.
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DeeptoolsTools to process and analyze deep sequencing data.
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chromapFast alignment and preprocessing of chromatin profiles
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DkmDynamic Kernel Matching (DKM) for Classifying Data with Non-conforming Features
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plasmidtronAssembling the cause of phenotypes and genotypes from NGS data
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GoatoolsPython library to handle Gene Ontology (GO) terms
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Quota AlignmentGuided synteny alignment between duplicated genomes (within specified quota constraint)
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FALDOFeature Annotation Location Description Ontology
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Bwa Mem2The next version of bwa-mem
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smartas📓Notebook of Climente-González et al. (2017), The Functional Impact of Alternative Splicing in Cancer.
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Fastq.bioAn interactive web tool for quality control of DNA sequencing data
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staramrScans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
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JbrowseA modern genome browser built with JavaScript and HTML5.
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calN50Compute N50/NG50 and auN/auNG
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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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catchA package for designing compact and comprehensive capture probe sets.
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MegahitUltra-fast and memory-efficient (meta-)genome assembler
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saffrontreeSaffronTree: Reference free rapid phylogenetic tree construction from raw read data
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BioBioinformatics library for .NET
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echtvarecht rapid variant annotation and filtering
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PyfaidxEfficient pythonic random access to fasta subsequences
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RadiatorRADseq Data Exploration, Manipulation and Visualization using R
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wdlRunRElastic, reproducible, and reusable genomic data science tools from R backed by cloud resources
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ArvadosAn open source platform for managing and analyzing biomedical big data
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perfPERF is an Exhaustive Repeat Finder
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GubbinsRapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
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dysgudysgu-SV is a collection of tools for calling structural variants using short or long reads
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PygenoPersonalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
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wgs2ncbiToolkit for preparing genomes for submission to NCBI
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BwaBurrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
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faster lmm dA faster lmm for GWAS. Supports GPU backend.
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Vcfannoannotate a VCF with other VCFs/BEDs/tabixed files
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bio-pipelineMy collection of light bioinformatics analysis pipelines for specific tasks
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Awesome 10x GenomicsList of tools and resources related to the 10x Genomics GEMCode/Chromium system
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open-cravatA modular annotation tool for genomic variants
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Eggnog MapperFast genome-wide functional annotation through orthology assignment
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hts-pythonpythonic wrapper for htslib
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souporcellClustering scRNAseq by genotypes
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jbrowse-componentsMonorepo with JBrowse 2 web, JBrowse 2 desktop, the JB core package, and core plugins. To customize behaviors, write an in-house plugin.
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Deep ReviewA collaboratively written review paper on deep learning, genomics, and precision medicine
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gff3toemblConverts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
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ScoaryPan-genome wide association studies
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Dna NnModel and predict short DNA sequence features with neural networks
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fermikitDe novo assembly based variant calling pipeline for Illumina short reads
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