koverLearn interpretable computational phenotyping models from k-merized genomic data
Stars: ✭ 47 (-30.88%)
PyfaidxEfficient pythonic random access to fasta subsequences
Stars: ✭ 307 (+351.47%)
HgvsPython library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
Stars: ✭ 138 (+102.94%)
IntermineA powerful open source data warehouse system
Stars: ✭ 195 (+186.76%)
SarekDetect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
Stars: ✭ 124 (+82.35%)
VcfrTools to work with variant call format files
Stars: ✭ 149 (+119.12%)
FlowcraftFlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦
Stars: ✭ 208 (+205.88%)
Hts Nimnim wrapper for htslib for parsing genomics data files
Stars: ✭ 132 (+94.12%)
DragonnA toolkit to learn how to model and interpret regulatory sequence data using deep learning.
Stars: ✭ 222 (+226.47%)
NglessNGLess: NGS with less work
Stars: ✭ 115 (+69.12%)
IdeogramChromosome visualization for the web
Stars: ✭ 181 (+166.18%)
Slivarvariant expressions, annotation, and filtering for great good.
Stars: ✭ 110 (+61.76%)
GlowAn open-source toolkit for large-scale genomic analysis
Stars: ✭ 159 (+133.82%)
GenomeworksSDK for GPU accelerated genome assembly and analysis
Stars: ✭ 215 (+216.18%)
BiomartrGenomic Data Retrieval with R
Stars: ✭ 144 (+111.76%)
BiopythonOfficial git repository for Biopython (originally converted from CVS)
Stars: ✭ 2,936 (+4217.65%)
HifiasmHifiasm: a haplotype-resolved assembler for accurate Hifi reads
Stars: ✭ 134 (+97.06%)
JuicerA One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Stars: ✭ 203 (+198.53%)
Benchmarking ToolsRepository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
Stars: ✭ 129 (+89.71%)
cljamA DNA Sequence Alignment/Map (SAM) library for Clojure
Stars: ✭ 85 (+25%)
CirclatorA tool to circularize genome assemblies
Stars: ✭ 121 (+77.94%)
GenometoolsGenomeTools genome analysis system.
Stars: ✭ 186 (+173.53%)
CoolerA cool place to store your Hi-C
Stars: ✭ 112 (+64.71%)
HtsjdkA Java API for high-throughput sequencing data (HTS) formats.
Stars: ✭ 220 (+223.53%)
GenomicsA collection of scripts and notes related to genomics and bioinformatics
Stars: ✭ 101 (+48.53%)
Deep RulesTen Quick Tips for Deep Learning in Biology
Stars: ✭ 179 (+163.24%)
AribaAntimicrobial Resistance Identification By Assembly
Stars: ✭ 96 (+41.18%)
Goleftgoleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
Stars: ✭ 175 (+157.35%)
Bedops🔬 BEDOPS: high-performance genomic feature operations
Stars: ✭ 215 (+216.18%)
Viral NgsViral genomics analysis pipelines
Stars: ✭ 150 (+120.59%)
CanvasxpressJavaScript VisualizationTools
Stars: ✭ 247 (+263.24%)
Smoovestructural variant calling and genotyping with existing tools, but, smoothly.
Stars: ✭ 147 (+116.18%)
HiglassFast large scale matrix visualization for the web.
Stars: ✭ 208 (+205.88%)
fermiA WGS de novo assembler based on the FMD-index for large genomes
Stars: ✭ 74 (+8.82%)
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 (+98.53%)
MinigraphProof-of-concept seq-to-graph mapper and graph generator
Stars: ✭ 206 (+202.94%)
OctopusBayesian haplotype-based mutation calling
Stars: ✭ 131 (+92.65%)
Cyvcf2cython + htslib == fast VCF and BCF processing
Stars: ✭ 243 (+257.35%)
Miso LimsMISO: An open-source LIMS for NGS sequencing centres
Stars: ✭ 131 (+92.65%)
SequenceserverIntuitive local web frontend for the BLAST bioinformatics tool
Stars: ✭ 198 (+191.18%)
Somalierfast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
Stars: ✭ 128 (+88.24%)
HLAxHLA: Fast and accurate HLA typing from short read sequence data
Stars: ✭ 84 (+23.53%)
Kmer CntCode examples of fast and simple k-mer counters for tutorial purposes
Stars: ✭ 124 (+82.35%)
DeepvariantDeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Stars: ✭ 2,404 (+3435.29%)
HicexplorerHiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
Stars: ✭ 116 (+70.59%)
BowtieAn ultrafast memory-efficient short read aligner
Stars: ✭ 221 (+225%)
QqmanAn R package for creating Q-Q and manhattan plots from GWAS results
Stars: ✭ 115 (+69.12%)
RibbonA genome browser that shows long reads and complex variants better
Stars: ✭ 184 (+170.59%)
CgrangesA C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)
Stars: ✭ 111 (+63.24%)
raptorA fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.
Stars: ✭ 37 (-45.59%)
MsprimeSimulate genealogical trees and genomic sequence data using population genetic models
Stars: ✭ 103 (+51.47%)
Janggu Deep learning infrastructure for bioinformatics
Stars: ✭ 174 (+155.88%)
SmudgeplotInference of ploidy and heterozygosity structure using whole genome sequencing data
Stars: ✭ 98 (+44.12%)
PyrangesPerformant Pythonic GenomicRanges
Stars: ✭ 219 (+222.06%)
WgsimReads simulator
Stars: ✭ 178 (+161.76%)
MittySeven Bridges Genomics aligner/caller debugging and analysis tools
Stars: ✭ 13 (-80.88%)
Hap.pyHaplotype VCF comparison tools
Stars: ✭ 249 (+266.18%)