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Vcfannoannotate a VCF with other VCFs/BEDs/tabixed files
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Bwa Mem2The next version of bwa-mem
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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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BwaBurrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
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Vgtools for working with genome variation graphs
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GoatoolsPython library to handle Gene Ontology (GO) terms
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dna-traitsA fast 23andMe genome text file parser, now superseded by arv
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RadiatorRADseq Data Exploration, Manipulation and Visualization using R
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JbrowseA modern genome browser built with JavaScript and HTML5.
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PyfaidxEfficient pythonic random access to fasta subsequences
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PygenoPersonalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
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BgdataA Suite of Packages for Analysis of Big Genomic Data
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Quota AlignmentGuided synteny alignment between duplicated genomes (within specified quota constraint)
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NucleusPython and C++ code for reading and writing genomics data.
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coolpuppyA versatile tool to perform pile-up analysis on Hi-C data in .cool format.
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Vcflib C++ library and cmdline tools for parsing and manipulating VCF files
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Dna NnModel and predict short DNA sequence features with neural networks
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JcviPython library to facilitate genome assembly, annotation, and comparative genomics
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Bowtie2A fast and sensitive gapped read aligner
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JvarkitJava utilities for Bioinformatics
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Minimap2A versatile pairwise aligner for genomic and spliced nucleotide sequences
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Sixess🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files
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PostguiA React web application to query and share any PostgreSQL database.
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Bio.jl[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
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PHANOTATEPHANOTATE: a tool to annotate phage genomes.
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GalaxyData intensive science for everyone.
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mccortexDe novo genome assembly and multisample variant calling
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fermikitDe novo assembly based variant calling pipeline for Illumina short reads
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HailScalable genomic data analysis.
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SnsAnalysis pipelines for sequencing data
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SvtyperBayesian genotyper for structural variants
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Fastq.bioAn interactive web tool for quality control of DNA sequencing data
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Deep ReviewA collaboratively written review paper on deep learning, genomics, and precision medicine
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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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DeeptoolsTools to process and analyze deep sequencing data.
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