HailScalable genomic data analysis.
Stars: ✭ 706 (+793.67%)
GenomicsA collection of scripts and notes related to genomics and bioinformatics
Stars: ✭ 101 (+27.85%)
Tiledb VcfEfficient variant-call data storage and retrieval library using the TileDB storage library.
Stars: ✭ 26 (-67.09%)
Hap.pyHaplotype VCF comparison tools
Stars: ✭ 249 (+215.19%)
Vcfannoannotate a VCF with other VCFs/BEDs/tabixed files
Stars: ✭ 259 (+227.85%)
Cyvcf2cython + htslib == fast VCF and BCF processing
Stars: ✭ 243 (+207.59%)
PygenoPersonalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Stars: ✭ 261 (+230.38%)
plasmidtronAssembling the cause of phenotypes and genotypes from NGS data
Stars: ✭ 27 (-65.82%)
TypeTEGenotyping of segregating mobile elements insertions
Stars: ✭ 15 (-81.01%)
BgtFlexible genotype query among 30,000+ samples whole-genome
Stars: ✭ 72 (-8.86%)
fermikitDe novo assembly based variant calling pipeline for Illumina short reads
Stars: ✭ 98 (+24.05%)
GubbinsRapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Stars: ✭ 67 (-15.19%)
GenomicDataCommonsProvide R access to the NCI Genomic Data Commons portal.
Stars: ✭ 64 (-18.99%)
netSmoothnetSmooth: A Network smoothing based method for Single Cell RNA-seq imputation
Stars: ✭ 23 (-70.89%)
reg-genRegulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
Stars: ✭ 64 (-18.99%)
EarlGreyEarl Grey: A fully automated TE curation and annotation pipeline
Stars: ✭ 25 (-68.35%)
bacnetBACNET is a Java based platform to develop website for multi-omics analysis
Stars: ✭ 12 (-84.81%)
awesome-geneticsA curated list of awesome bioinformatics software.
Stars: ✭ 60 (-24.05%)
Bio.jl[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
Stars: ✭ 257 (+225.32%)
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 (-75.95%)
PostguiA React web application to query and share any PostgreSQL database.
Stars: ✭ 260 (+229.11%)
Dna NnModel and predict short DNA sequence features with neural networks
Stars: ✭ 59 (-25.32%)
JvarkitJava utilities for Bioinformatics
Stars: ✭ 313 (+296.2%)
MegahitUltra-fast and memory-efficient (meta-)genome assembler
Stars: ✭ 343 (+334.18%)
Bowtie2A fast and sensitive gapped read aligner
Stars: ✭ 365 (+362.03%)
Biojava📖🔬☕️ BioJava is an open-source project dedicated to providing a Java library for processing biological data.
Stars: ✭ 434 (+449.37%)
bystroBystro genetic analysis (annotation, filtering, statistics)
Stars: ✭ 31 (-60.76%)
DramDistilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
Stars: ✭ 47 (-40.51%)
SVCollectorMethod to optimally select samples for validation and resequencing
Stars: ✭ 20 (-74.68%)
SnsAnalysis pipelines for sequencing data
Stars: ✭ 43 (-45.57%)
chromapFast alignment and preprocessing of chromatin profiles
Stars: ✭ 93 (+17.72%)
Fastq.bioAn interactive web tool for quality control of DNA sequencing data
Stars: ✭ 76 (-3.8%)
staramrScans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Stars: ✭ 52 (-34.18%)
dna-traitsA fast 23andMe genome text file parser, now superseded by arv
Stars: ✭ 64 (-18.99%)
tiptoftPredict plasmids from uncorrected long read data
Stars: ✭ 27 (-65.82%)
GatkOfficial code repository for GATK versions 4 and up
Stars: ✭ 1,002 (+1168.35%)
OntologiesHome of the Genomic Feature and Variation Ontology (GFVO)
Stars: ✭ 16 (-79.75%)
gff3toemblConverts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
Stars: ✭ 27 (-65.82%)
companionThis repository has been archived, currently maintained version is at https://github.com/iii-companion/companion
Stars: ✭ 21 (-73.42%)
JbrowseA modern genome browser built with JavaScript and HTML5.
Stars: ✭ 393 (+397.47%)
DeeptoolsTools to process and analyze deep sequencing data.
Stars: ✭ 448 (+467.09%)
HtslibC library for high-throughput sequencing data formats
Stars: ✭ 529 (+569.62%)
PyfaidxEfficient pythonic random access to fasta subsequences
Stars: ✭ 307 (+288.61%)
Gwa tutorialA comprehensive tutorial about GWAS and PRS
Stars: ✭ 303 (+283.54%)
BwaBurrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Stars: ✭ 970 (+1127.85%)
ArvadosAn open source platform for managing and analyzing biomedical big data
Stars: ✭ 274 (+246.84%)
Bwa Mem2The next version of bwa-mem
Stars: ✭ 408 (+416.46%)
JcviPython library to facilitate genome assembly, annotation, and comparative genomics
Stars: ✭ 404 (+411.39%)
SeqA high-performance, Pythonic language for bioinformatics
Stars: ✭ 263 (+232.91%)
Helmsmanhighly-efficient & lightweight mutation signature matrix aggregation
Stars: ✭ 19 (-75.95%)
GalaxyData intensive science for everyone.
Stars: ✭ 812 (+927.85%)
16gtSimultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
Stars: ✭ 26 (-67.09%)
GenozipCompressor for genomic files (FASTQ, SAM/BAM, VCF, FASTA, GVF, 23andMe...), up to 5x better than gzip and faster too
Stars: ✭ 53 (-32.91%)
catchA package for designing compact and comprehensive capture probe sets.
Stars: ✭ 55 (-30.38%)
calN50Compute N50/NG50 and auN/auNG
Stars: ✭ 20 (-74.68%)
Minimap2A versatile pairwise aligner for genomic and spliced nucleotide sequences
Stars: ✭ 912 (+1054.43%)