Topic: genome Goto Github

👇 Here are 416 public repositories matching this topic...

aehrc / variantspark
genome,machine learning for genomic variants
Organization: aehrc
Home Page: http://bioinformatics.csiro.au/variantspark
variant-spark gwas random-forest genome association-studies vcf variantspark notebook databricks bioinformatics

alekseyzimin / masurca
genome,
User: alekseyzimin
masurca genome assembly bioinformatics

althonos / pyrodigal
genome,Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
User: althonos
Home Page: https://pyrodigal.readthedocs.org
orf-finder metagenomes python bioconda python-library cython-wrapper python-interface prodigal genome gene-finding

aquaskyline / soapdenovo2
genome,Next generation sequencing reads de novo assembler.
User: aquaskyline
bioinformatics assembly soapdenovo genome computational-biology

ay-lab / dchic
genome,dcHiC: Differential compartment analysis for Hi-C datasets
User: ay-lab
hi-c bioinformatics genome chromatin

bcgsc / abyss
genome,:microscope: Assemble large genomes using short reads
Organization: bcgsc
Home Page: http://www.bcgsc.ca/platform/bioinfo/software/abyss
bloom-filter c-plus-plus science bioinformatics assembler scaffold genome openmp mpi

bcgsc / arcs
genome,🌈Scaffold genome sequence assemblies using linked or long read sequencing data
Organization: bcgsc
c-plus-plus science bioinformatics assembler scaffold genome 10xgenomics graph nanopore-sequencing oxford-nanopore pacbio-data

bcgsc / nanosim
genome,Nanopore sequence read simulator
Organization: bcgsc
genome transcriptome simulator oxford-nanopore nanopore-sequencing

bernatgel / karyoploter
genome,karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
User: bernatgel
Home Page: https://bernatgel.github.io/karyoploter_tutorial/
bioconductor genome rstats data-visualization plotting-in-r genomics-visualization bioinformatics

brentp / mosdepth
genome,fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
User: brentp
coverage genome depth exome wgs sequencing nim nim-lang hacktoberfest

broadinstitute / catch
genome,A package for designing compact and comprehensive capture probe sets.
Organization: broadinstitute
science genomics genome viral sequencing ngs dna bioinformatics metagenomics covid-19

broadinstitute / gatk
genome,Official code repository for GATK versions 4 and up
Organization: broadinstitute
Home Page: https://software.broadinstitute.org/gatk
genomics spark science dna ngs sequencing genome bioinformatics gatk

broadinstitute / viral-ngs
genome,Viral genomics analysis pipelines
Organization: broadinstitute
viral-ngs viral genomics genome genome-assembly genome-sequencing bam fastq variant-calling variant-annotations

combine-lab / pufferfish
genome,An efficient index for the colored, compacted, de Bruijn graph
Organization: combine-lab
debruijn-graph debruijn index hash contigs genome dbg

cslarsen / arv
genome,A fast 23andMe DNA parser and inferrer for Python
User: cslarsen
23andme dna python genome bioinformatics snpedia snps

decipher-genomics / genoverse
genome,HTML5 scrollable genome browser
Organization: decipher-genomics
Home Page: https://genoverse.org/
genome visualisation

flowhub-team / cnv
genome,Copy Number Variation
User: flowhub-team
cnv copy-number-variation copynumbervariation genome genomics

flowhub-team / wholegenomesequencing-wgs
genome,Whole Genome Sequencing analysis, WGS analysis
User: flowhub-team
bioinfomatics bioinformatics-pipeline genome wes wgs whole-genome-sequencing

gaius-augustus / augustus
genome,Genome annotation with AUGUSTUS
Organization: gaius-augustus
Home Page: http://bioinf.uni-greifswald.de/webaugustus/
genome annotation gene prediction discovery

genometools / genometools
genome,GenomeTools genome analysis system.
Organization: genometools
Home Page: http://genometools.org
genome bioinformatics gff3 genomics library annotation repeats python ruby lua

genotoul-bioinfo / dgenies
genome,Dotplot large Genomes in an Interactive, Efficient and Simple way
Organization: genotoul-bioinfo
Home Page: http://dgenies.toulouse.inrae.fr
inra genotoul bioinformatics dotplot genome comparision inrae

google / deepsomatic
genome,DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data.
Organization: google
bioinformatics deep-learning dna genome genomics machine science sequencing somatic-mutations somatic-variants deepsomatic

google / deepvariant
genome,DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Organization: google
tensorflow deep-neural-network genomics science dna sequencing genome bioinformatics deep-learning ngs

hicai-zju / scientific-llm-survey
genome,Scientific Large Language Models: A Survey on Biological & Chemical Domains
Organization: hicai-zju
genome llms molecule multimodal protein science-research text sci-llm cell scientific-languages

icebert / pblat
genome,parallelized blat with multi-threads support
User: icebert
Home Page: http://icebert.github.io/pblat/
alignment genome mapping multithreading parallel sequencing

ivanseidel / iamdinosaur
genome,🦄 An Artificial Inteligence to teach Google's Dinosaur to jump cactus
User: ivanseidel
neural-network genome dino genetic-algorithm google-dinosaur artificial-intelligence

jasperlinthorst / reveal
genome,Graph based multi genome aligner
User: jasperlinthorst
gfa graph alignment genome assembly reveal multiple-sequence-alignment

jerryji1993 / dnabert
genome,DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
User: jerryji1993
Home Page: https://doi.org/10.1093/bioinformatics/btab083
kmer dnabert-model kmer-format gpu sequence genome machine-learning deep-learning natural-language-processing nlp

kennethreitz / context
genome,Raw dump of Kenneth Reitz's DNA Sequence, Ancestry, Genealogy, &c.
User: kennethreitz
Home Page: https://context.kennethreitz.org/
genome human-genome kennethreitz 23andme promethease geneology gedcom gedcom-files ancestry dna

lmdu / pyfastx
genome,a python package for fast random access to sequences from plain and gzipped FASTA/Q files
User: lmdu
Home Page: https://pyfastx.readthedocs.io
fasta python biology dna genome assembly sequence fastq bioinformatics

magics-lab / dnabert_2
genome,[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
Organization: magics-lab
dataset dna dna-processing dna-training genome genome-analysis language-model covid promoter promoter-analysis

marianattestad / ribbon
genome,A genome browser that shows long reads and complex variants better
User: marianattestad
Home Page: http://genomeribbon.com
bioinformatics genome genomics visualization

mentatpsi / osgenome
genome,An Open Source Web Application for Genetic Data (SNPs) using 23AndMe and Data Crawling Technologies
User: mentatpsi
23andme snps genome data-crawling python genetic-data kendo flask genetics snpedia

mobinasri / flagger
genome,Evaluating genome assemblies
User: mobinasri
bioinformatics genome-assembly-evaluation genomics genome

muellan / metacache
genome,memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
User: muellan
genome read-mapping refseq taxonomy metagenomics metagenomic-analysis metagenomic-classification metagenomes metagenomic-data ncbi-refseq

neherlab / pangraph
genome,A bioinformatic toolkit to align genome assemblies into pangenome graphs
Organization: neherlab
Home Page: https://neherlab.github.io/pangraph
bioinformatics genome julia pangraph genome-assembly pangenome bacteria

nextomics / nextpolish
genome, Fast and accurately polish the genome generated by long reads.
Organization: nextomics
genome polish assembly

nf-core / eager
genome,A fully reproducible and state-of-the-art ancient DNA analysis pipeline
Organization: nf-core
Home Page: https://nf-co.re/eager
nextflow ancientdna adna pipeline pathogen-genomics population-genetics nf-core workflow metagenomics bioinformatics

pirovc / genome_updater
genome,Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy
User: pirovc
bioinformatics ncbi bash genome sequence refseq genbank download database genomes

primaryobjects / ai-programmer
genome,Using artificial intelligence and genetic algorithms to automatically write programs. Tutorial: http://www.primaryobjects.com/cms/article149
User: primaryobjects
genetic-algorithms c-sharp fitness-score ai artificial-intelligence genetic-algorithm genetic-programming programming-language genome program-synthesis

quxiaojian / pga
genome,Plastid Genome Annotator
User: quxiaojian
chloroplast plastid plastome genome annotation

rnabioco / valr
genome,Genome Interval Arithmetic in R
Organization: rnabioco
Home Page: http://rnabioco.github.io/valr/
genome interval-arithmetic bedtools

robert-koch-institut / sars-cov-2-sequenzdaten_aus_deutschland
genome,Das Robert Koch-Institut stellt Systeme zur bundesweiten molekularen Surveillance des SARS-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 übermitteln.
Organization: robert-koch-institut
Home Page: https://robert-koch-institut.github.io/SARS-CoV-2-Sequenzdaten_aus_Deutschland/
covid-19 sars-cov-2 virusstrukturen genom basensequenz deutschland viral-structures genome base-sequence germany

ropensci / biomartr
genome,Genomic Data Retrieval with R
Organization: ropensci
Home Page: https://docs.ropensci.org/biomartr
r genome-retrieval biomart database-retrieval ncbi-genbank genomics ensembl-servers sequenced-genomes proteome genome

samtobam / mumandco
genome,MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (only v4) to detect Structural Variation
User: samtobam
sv-detection mummer genome structural-variation

tariqdaouda / pygeno
genome,Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
User: tariqdaouda
Home Page: http://pygeno.iric.ca
bioinformatics biology genomics proteomics genome genome-annotation genome-browser genome-sequencing genomes medical

tolkit / telomeric-identifier
genome,Identify and find telomeres, or telomeric repeats in a genome.
Organization: tolkit
genome rust telomere repeats telomeric telomeres bioinformatics

vanheeringen-lab / genomepy
genome,genes and genomes at your fingertips
Organization: vanheeringen-lab
Home Page: https://vanheeringen-lab.github.io/genomepy/
bioconda ensembl genome ncbi python ucsc

zengxiaofei / haphic
genome,HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data
User: zengxiaofei
assembly chromosome genome hi-c scaffolding haplotype phasing 3d-dna lachesis salsa

zhaotao1987 / synnet-pipeline
genome,Workflow for Building Microsynteny Networks
User: zhaotao1987
synteny-network phylogenomics genome network-analysis