GenomicDataCommonsProvide R access to the NCI Genomic Data Commons portal.
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Bio.jl[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
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gff3toemblConverts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
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saffrontreeSaffronTree: Reference free rapid phylogenetic tree construction from raw read data
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JcviPython library to facilitate genome assembly, annotation, and comparative genomics
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bystroBystro genetic analysis (annotation, filtering, statistics)
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dna-traitsA fast 23andMe genome text file parser, now superseded by arv
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EarlGreyEarl Grey: A fully automated TE curation and annotation pipeline
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Bowtie2A fast and sensitive gapped read aligner
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wdlRunRElastic, reproducible, and reusable genomic data science tools from R backed by cloud resources
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Dna NnModel and predict short DNA sequence features with neural networks
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simplesamSimple pure Python SAM parser and objects for working with SAM records
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staramrScans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
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catchA package for designing compact and comprehensive capture probe sets.
Stars: ✭ 55 (-23.61%)
netSmoothnetSmooth: A Network smoothing based method for Single Cell RNA-seq imputation
Stars: ✭ 23 (-68.06%)
awesome-geneticsA curated list of awesome bioinformatics software.
Stars: ✭ 60 (-16.67%)
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.
Stars: ✭ 19 (-73.61%)
plasmidtronAssembling the cause of phenotypes and genotypes from NGS data
Stars: ✭ 27 (-62.5%)
DramDistilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
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Gwa tutorialA comprehensive tutorial about GWAS and PRS
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SnsAnalysis pipelines for sequencing data
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PyfaidxEfficient pythonic random access to fasta subsequences
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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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GatkOfficial code repository for GATK versions 4 and up
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Tiledb VcfEfficient variant-call data storage and retrieval library using the TileDB storage library.
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dysgudysgu-SV is a collection of tools for calling structural variants using short or long reads
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ntHashFast hash function for DNA sequences
Stars: ✭ 66 (-8.33%)
unimapA EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment
Stars: ✭ 76 (+5.56%)
companionThis repository has been archived, currently maintained version is at https://github.com/iii-companion/companion
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calN50Compute N50/NG50 and auN/auNG
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wgs2ncbiToolkit for preparing genomes for submission to NCBI
Stars: ✭ 25 (-65.28%)
BwaBurrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Stars: ✭ 970 (+1247.22%)
chromapFast alignment and preprocessing of chromatin profiles
Stars: ✭ 93 (+29.17%)
tiptoftPredict plasmids from uncorrected long read data
Stars: ✭ 27 (-62.5%)
reg-genRegulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
Stars: ✭ 64 (-11.11%)
fermikitDe novo assembly based variant calling pipeline for Illumina short reads
Stars: ✭ 98 (+36.11%)
bacnetBACNET is a Java based platform to develop website for multi-omics analysis
Stars: ✭ 12 (-83.33%)
Scaff10XPipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads
Stars: ✭ 21 (-70.83%)
ArvadosAn open source platform for managing and analyzing biomedical big data
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SeqA high-performance, Pythonic language for bioinformatics
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Minimap2A versatile pairwise aligner for genomic and spliced nucleotide sequences
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PygenoPersonalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
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MegahitUltra-fast and memory-efficient (meta-)genome assembler
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JvarkitJava utilities for Bioinformatics
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JbrowseA modern genome browser built with JavaScript and HTML5.
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PostguiA React web application to query and share any PostgreSQL database.
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DeeptoolsTools to process and analyze deep sequencing data.
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GalaxyData intensive science for everyone.
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Biojava📖🔬☕️ BioJava is an open-source project dedicated to providing a Java library for processing biological data.
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jgi-queryA simple command-line tool to download data from Joint Genome Institute databases
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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
Stars: ✭ 259 (+259.72%)
Bwa Mem2The next version of bwa-mem
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GubbinsRapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
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