DeepvariantDeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
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catchA package for designing compact and comprehensive capture probe sets.
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GalaxyData intensive science for everyone.
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GenomicsA collection of scripts and notes related to genomics and bioinformatics
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UgeneUGENE is free open-source cross-platform bioinformatics software
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SnsAnalysis pipelines for sequencing data
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HtsjdkA Java API for high-throughput sequencing data (HTS) formats.
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NglessNGLess: NGS with less work
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JvarkitJava utilities for Bioinformatics
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dna-traitsA fast 23andMe genome text file parser, now superseded by arv
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awesome-geneticsA curated list of awesome bioinformatics software.
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Scaff10XPipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads
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BiopythonOfficial git repository for Biopython (originally converted from CVS)
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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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GubbinsRapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
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Arcs🌈Scaffold genome sequence assemblies using linked read sequencing data
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Bio.jl[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
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FastpAn ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
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Fastq.bioAn interactive web tool for quality control of DNA sequencing data
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CirclatorA tool to circularize genome assemblies
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PygenoPersonalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
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PyfaidxEfficient pythonic random access to fasta subsequences
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RibbonA genome browser that shows long reads and complex variants better
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PHATPathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform
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GenometoolsGenomeTools genome analysis system.
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SequenceserverIntuitive local web frontend for the BLAST bioinformatics tool
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gencoreGenerate duplex/single consensus reads to reduce sequencing noises and remove duplications
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HgvsPython library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
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DeeptoolsTools to process and analyze deep sequencing data.
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Abyss🔬 Assemble large genomes using short reads
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NucleusPython and C++ code for reading and writing genomics data.
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HailScalable genomic data analysis.
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AribaAntimicrobial Resistance Identification By Assembly
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saffrontreeSaffronTree: Reference free rapid phylogenetic tree construction from raw read data
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adaptA package for designing activity-informed nucleic acid diagnostics for viruses.
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Tiledb VcfEfficient variant-call data storage and retrieval library using the TileDB storage library.
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gff3toemblConverts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
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reg-genRegulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
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MGSEMapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.
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RoaryRapid large-scale prokaryote pan genome analysis
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Rnaseq WorkflowA repository for setting up a RNAseq workflow
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plasmidtronAssembling the cause of phenotypes and genotypes from NGS data
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AfterqcAutomatic Filtering, Trimming, Error Removing and Quality Control for fastq data
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ArtemisArtemis 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
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STingUltrafast sequence typing and gene detection from NGS raw reads
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companionThis repository has been archived, currently maintained version is at https://github.com/iii-companion/companion
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MigmapHTS-compatible wrapper for IgBlast V-(D)-J mapping tool
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fastq utilsValidation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.
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tiptoftPredict plasmids from uncorrected long read data
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netSmoothnetSmooth: A Network smoothing based method for Single Cell RNA-seq imputation
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peppyProject metadata manager for PEPs in Python
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bacnetBACNET is a Java based platform to develop website for multi-omics analysis
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fermikitDe novo assembly based variant calling pipeline for Illumina short reads
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BwaBurrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
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chromapFast alignment and preprocessing of chromatin profiles
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EarlGreyEarl Grey: A fully automated TE curation and annotation pipeline
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ctdna-pipelineA simplified pipeline for ctDNA sequencing data analysis
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