Abyss🔬 Assemble large genomes using short reads
GenomepyDownload and use genomes the easy way.
DeepvariantDeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
KaryoploterkaryoploteR - An R/Bioconductor package to plot arbitrary data along the genome
RibbonA genome browser that shows long reads and complex variants better
Soapdenovo2Next generation sequencing reads de novo assembler.
Arcs🌈Scaffold genome sequence assemblies using linked read sequencing data
GatkOfficial code repository for GATK versions 4 and up
Ai ProgrammerUsing artificial intelligence and genetic algorithms to automatically write programs. Tutorial: http://www.primaryobjects.com/cms/article149
16gtSimultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
Metacachememory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
Mosdepthfast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
PygenoPersonalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Iamdinosaur🦄 An Artificial Inteligence to teach Google's Dinosaur to jump cactus
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.
pblatparallelized blat with multi-threads support
companionThis repository has been archived, currently maintained version is at https://github.com/iii-companion/companion
catchA package for designing compact and comprehensive capture probe sets.
perfPERF is an Exhaustive Repeat Finder
MUMandCoMUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (only v4) to detect Structural Variation
Scaff10XPipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads
revealGraph based multi genome aligner
pufferfishAn efficient index for the colored, compacted, de Bruijn graph
polioResearch on polio / protein folding.
dcHiCdcHiC: Differential compartment analysis for Hi-C datasets
SARS-CoV-2-Sequenzdaten aus DeutschlandDas Robert Koch-Institut stellt Systeme zur bundesweiten molekularen Surveillance des SRARS-CoV-2-Virus bereit. Jedes Labor in Deutschland, das SARS-CoV-2 sequenziert, ist laut der Verordnung zur molekulargenetischen Surveillance des Coronavirus SARS-CoV-2 verpflichtet, dem Robert Koch-Institut die Sequenz- und zugehörige Metadaten zu übermittel…
pyrodigalCython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
NanoSimNanopore sequence read simulator
arvA fast 23andMe DNA parser and inferrer for Python
valrGenome Interval Arithmetic in R
LTRpredDe novo annotation of young retrotransposons
MGSEMapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.
genome updaterBash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy