EarlGreyEarl Grey: A fully automated TE curation and annotation pipeline
Stars: ✭ 25 (+19.05%)
wgs2ncbiToolkit for preparing genomes for submission to NCBI
Stars: ✭ 25 (+19.05%)
RibbonA genome browser that shows long reads and complex variants better
Stars: ✭ 184 (+776.19%)
Hap.pyHaplotype VCF comparison tools
Stars: ✭ 249 (+1085.71%)
LRSDAYLRSDAY: Long-read Sequencing Data Analysis for Yeasts
Stars: ✭ 26 (+23.81%)
gff3toemblConverts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
Stars: ✭ 27 (+28.57%)
Deep RulesTen Quick Tips for Deep Learning in Biology
Stars: ✭ 179 (+752.38%)
MiniasmUltrafast de novo assembly for long noisy reads (though having no consensus step)
Stars: ✭ 216 (+928.57%)
BowtieAn ultrafast memory-efficient short read aligner
Stars: ✭ 221 (+952.38%)
dysgudysgu-SV is a collection of tools for calling structural variants using short or long reads
Stars: ✭ 47 (+123.81%)
saffrontreeSaffronTree: Reference free rapid phylogenetic tree construction from raw read data
Stars: ✭ 17 (-19.05%)
bacnetBACNET is a Java based platform to develop website for multi-omics analysis
Stars: ✭ 12 (-42.86%)
HgvsPython library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
Stars: ✭ 138 (+557.14%)
WgsimReads simulator
Stars: ✭ 178 (+747.62%)
Goleftgoleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
Stars: ✭ 175 (+733.33%)
tiptoftPredict plasmids from uncorrected long read data
Stars: ✭ 27 (+28.57%)
MinigraphProof-of-concept seq-to-graph mapper and graph generator
Stars: ✭ 206 (+880.95%)
CanvasxpressJavaScript VisualizationTools
Stars: ✭ 247 (+1076.19%)
GenometoolsGenomeTools genome analysis system.
Stars: ✭ 186 (+785.71%)
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 (-9.52%)
unimapA EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment
Stars: ✭ 76 (+261.9%)
fermikitDe novo assembly based variant calling pipeline for Illumina short reads
Stars: ✭ 98 (+366.67%)
wdlRunRElastic, reproducible, and reusable genomic data science tools from R backed by cloud resources
Stars: ✭ 34 (+61.9%)
GenomicDataCommonsProvide R access to the NCI Genomic Data Commons portal.
Stars: ✭ 64 (+204.76%)
reg-genRegulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
Stars: ✭ 64 (+204.76%)
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
Stars: ✭ 135 (+542.86%)
HifiasmHifiasm: a haplotype-resolved assembler for accurate Hifi reads
Stars: ✭ 134 (+538.1%)
OctopusBayesian haplotype-based mutation calling
Stars: ✭ 131 (+523.81%)
dna-traitsA fast 23andMe genome text file parser, now superseded by arv
Stars: ✭ 64 (+204.76%)
RoaryRapid large-scale prokaryote pan genome analysis
Stars: ✭ 176 (+738.1%)
Janggu Deep learning infrastructure for bioinformatics
Stars: ✭ 174 (+728.57%)
Hts Nimnim wrapper for htslib for parsing genomics data files
Stars: ✭ 132 (+528.57%)
SequenceserverIntuitive local web frontend for the BLAST bioinformatics tool
Stars: ✭ 198 (+842.86%)
IntermineA powerful open source data warehouse system
Stars: ✭ 195 (+828.57%)
Bedops🔬 BEDOPS: high-performance genomic feature operations
Stars: ✭ 215 (+923.81%)
DeepvariantDeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Stars: ✭ 2,404 (+11347.62%)
BiopythonOfficial git repository for Biopython (originally converted from CVS)
Stars: ✭ 2,936 (+13880.95%)
Cyvcf2cython + htslib == fast VCF and BCF processing
Stars: ✭ 243 (+1057.14%)
gawnGenome Annotation Without Nightmares
Stars: ✭ 35 (+66.67%)
Somalierfast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
Stars: ✭ 128 (+509.52%)
Scaff10XPipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads
Stars: ✭ 21 (+0%)
faster lmm dA faster lmm for GWAS. Supports GPU backend.
Stars: ✭ 12 (-42.86%)
jgi-queryA simple command-line tool to download data from Joint Genome Institute databases
Stars: ✭ 38 (+80.95%)
netSmoothnetSmooth: A Network smoothing based method for Single Cell RNA-seq imputation
Stars: ✭ 23 (+9.52%)
ntHashFast hash function for DNA sequences
Stars: ✭ 66 (+214.29%)
simplesamSimple pure Python SAM parser and objects for working with SAM records
Stars: ✭ 50 (+138.1%)
catchA package for designing compact and comprehensive capture probe sets.
Stars: ✭ 55 (+161.9%)
TOGATOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.
Stars: ✭ 35 (+66.67%)
bystroBystro genetic analysis (annotation, filtering, statistics)
Stars: ✭ 31 (+47.62%)
staramrScans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Stars: ✭ 52 (+147.62%)
plasmidtronAssembling the cause of phenotypes and genotypes from NGS data
Stars: ✭ 27 (+28.57%)
companionThis repository has been archived, currently maintained version is at https://github.com/iii-companion/companion
Stars: ✭ 21 (+0%)
Kmer CntCode examples of fast and simple k-mer counters for tutorial purposes
Stars: ✭ 124 (+490.48%)
SarekDetect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
Stars: ✭ 124 (+490.48%)
GCModellerGCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language
Stars: ✭ 25 (+19.05%)
calN50Compute N50/NG50 and auN/auNG
Stars: ✭ 20 (-4.76%)
chromapFast alignment and preprocessing of chromatin profiles
Stars: ✭ 93 (+342.86%)
awesome-geneticsA curated list of awesome bioinformatics software.
Stars: ✭ 60 (+185.71%)