Goleftgoleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
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RoaryRapid large-scale prokaryote pan genome analysis
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Hts Nimnim wrapper for htslib for parsing genomics data files
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CoolerA cool place to store your Hi-C
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Bowtie2A fast and sensitive gapped read aligner
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SarekDetect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
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HailScalable genomic data analysis.
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GubbinsRapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
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SibeliazA fast whole-genome aligner based on de Bruijn graphs
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PygenoPersonalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
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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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SeqA high-performance, Pythonic language for bioinformatics
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MegahitUltra-fast and memory-efficient (meta-)genome assembler
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Gwa tutorialA comprehensive tutorial about GWAS and PRS
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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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Tiledb VcfEfficient variant-call data storage and retrieval library using the TileDB storage library.
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JcviPython library to facilitate genome assembly, annotation, and comparative genomics
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DramDistilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
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Dna NnModel and predict short DNA sequence features with neural networks
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BgtFlexible genotype query among 30,000+ samples whole-genome
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HgvsPython library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
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AribaAntimicrobial Resistance Identification By Assembly
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OctopusBayesian haplotype-based mutation calling
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CgrangesA C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)
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PostguiA React web application to query and share any PostgreSQL database.
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ArvadosAn open source platform for managing and analyzing biomedical big data
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Vcfannoannotate a VCF with other VCFs/BEDs/tabixed files
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JvarkitJava utilities for Bioinformatics
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PyfaidxEfficient pythonic random access to fasta subsequences
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JbrowseA modern genome browser built with JavaScript and HTML5.
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Bio.jl[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
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DeeptoolsTools to process and analyze deep sequencing data.
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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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NucleusPython and C++ code for reading and writing genomics data.
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Bwa Mem2The next version of bwa-mem
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GalaxyData intensive science for everyone.
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Kmer CntCode examples of fast and simple k-mer counters for tutorial purposes
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CirclatorA tool to circularize genome assemblies
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SnsAnalysis pipelines for sequencing data
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HicexplorerHiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
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GatkOfficial code repository for GATK versions 4 and up
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NglessNGLess: NGS with less work
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Fastq.bioAn interactive web tool for quality control of DNA sequencing data
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SvtyperBayesian genotyper for structural variants
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BwaBurrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
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BioBioinformatics library for .NET
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SmudgeplotInference of ploidy and heterozygosity structure using whole genome sequencing data
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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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gff3toemblConverts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
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Minimap2A versatile pairwise aligner for genomic and spliced nucleotide sequences
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Awesome 10x GenomicsList of tools and resources related to the 10x Genomics GEMCode/Chromium system
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GenomicsA collection of scripts and notes related to genomics and bioinformatics
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HifiasmHifiasm: a haplotype-resolved assembler for accurate Hifi reads
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