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genome

Here are 345 public repositories matching this topic...

ivanseidel / IAMDinosaur

🦄 An Artificial Inteligence to teach Google's Dinosaur to jump cactus

neural-network genome genetic-algorithm artificial-intelligence dino google-dinosaur

Updated Feb 7, 2018
JavaScript

google / deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

science machine-learning bioinformatics deep-learning genomics genome tensorflow ngs sequencing dna deep-neural-network deepvariant

Updated Jan 28, 2022
Python

broadinstitute / gatk

Official code repository for GATK versions 4 and up

java science bioinformatics spark genomics genome cluster ngs sequencing gatk-jar dna gatk

Updated Feb 25, 2022
Java

primaryobjects / AI-Programmer

Using artificial intelligence and genetic algorithms to automatically write programs. Tutorial: http://www.primaryobjects.com/cms/article149

c-sharp programming-language ai genome genetic-algorithm program-synthesis artificial-intelligence genetic-programming genetic-algorithms fitness-score

Updated Oct 7, 2020
C#

brentp / mosdepth

Sponsor

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

coverage nim genome sequencing depth wgs hacktoberfest exome nim-lang

Updated Feb 2, 2022
Nim

pyGeno

tariqdaouda / pyGeno

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Updated Sep 16, 2021
Python

bcgsc / abyss

🔬 Assemble large genomes using short reads

science c-plus-plus bioinformatics genome bloom-filter assembler scaffold openmp mpi

Updated Jan 18, 2022
C++

genomepy

vanheeringen-lab / genomepy

genes and genomes at your fingertips

python genome ensembl bioconda ucsc ncbi

Updated Feb 19, 2022
Python

bernatgel / karyoploteR

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

bioinformatics genome data-visualization rstats bioconductor genomics-visualization plotting-in-r

Updated Jan 19, 2022
R

genometools / genometools

GenomeTools genome analysis system.

ruby python c library bioinformatics lua annotation genomics genome gff3 repeats genometools toolkit

Updated Dec 10, 2021
C

jerryji1993 / DNABERT

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

nlp machine-learning natural-language-processing deep-learning genome gpu sequence kmer dnabert-model kmer-format

Updated Aug 27, 2021
Python

MariaNattestad / Ribbon

A genome browser that shows long reads and complex variants better

visualization bioinformatics genomics genome ribbon htdocs-folder

Updated Aug 14, 2021
JavaScript

aquaskyline / SOAPdenovo2

Next generation sequencing reads de novo assembler.

bioinformatics genome assembly computational-biology soapdenovo

Updated Apr 19, 2021
C

broadinstitute / viral-ngs

Viral genomics analysis pipelines

genomics genome variant-calling bam genome-sequencing illumina fastq genome-assembly variant-annotations viral-ngs viral

Updated Nov 3, 2020
Python

Gaius-Augustus / Augustus

Genome annotation with AUGUSTUS

gene annotation genome discovery prediction

Updated Feb 24, 2022
C++

alekseyzimin / masurca

bioinformatics genome assembly masurca

Updated Feb 17, 2022
M4

ropensci / biomartr

Genomic Data Retrieval with R

r genomics genome metagenomics rstats genome-annotation r-package meta-analysis genome-retrieval biomart database-retrieval ncbi-genbank ensembl-servers sequenced-genomes proteome peer-reviewed

Updated Feb 22, 2022
R

bcgsc / NanoSim

Nanopore sequence read simulator

simulator genome transcriptome oxford-nanopore nanopore-sequencing

Updated Feb 22, 2022
Python

lmdu / pyfastx

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

python bioinformatics genome biology assembly dna fasta sequence fastq

Updated Jul 30, 2021
C

Nextomics / NextPolish

Fast and accurately polish the genome generated by long reads.

genome assembly polish

Updated Oct 12, 2021

VariantSpark

aehrc / VariantSpark

machine learning for genomic variants

emr aws bioinformatics gwas genome random-forest notebook vcf databricks association-studies variant-spark variantspark

Updated Feb 23, 2022
JavaScript

cslarsen / arv

A fast 23andMe DNA parser and inferrer for Python

python bioinformatics snps genome dna snpedia 23andme

Updated Nov 9, 2019
C++

COMBINE-lab / pufferfish

An efficient index for the colored, compacted, de Bruijn graph

genome hash index debruijn dbg contigs debruijn-graph

Updated Feb 25, 2022
C++

context

kennethreitz / context

Raw dump of Kenneth Reitz's DNA Sequence, Ancestry, Genealogy, &c.

genome dna ancestry kennethreitz gedcom 23andme promethease gedcom-files geneology human-genome

Updated Oct 2, 2019
HTML

bcgsc / arcs

🌈Scaffold genome sequence assemblies using linked read sequencing data

science c-plus-plus bioinformatics genome graph assembler scaffold 10xgenomics

Updated Feb 11, 2022
C++

genotoul-bioinfo / dgenies

Dotplot large Genomes in an Interactive, Efficient and Simple way

bioinformatics genome inra comparision dotplot genotoul inrae

Updated Feb 25, 2022
Python

rnabioco / valr

Genome Interval Arithmetic in R

genome interval-arithmetic bedtools

Updated Feb 21, 2022
R

mentatpsi / OSGenome

An Open Source Web Application for Genetic Data (SNPs) using 23AndMe and Data Crawling Technologies

python flask snps genome genetics kendo snpedia raw-data 23andme genetic-data data-crawling

Updated Oct 15, 2021
Python

pirovc / genome_updater

Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

bash bioinformatics database genome download genbank sequence ncbi refseq

Updated Feb 3, 2022
Shell

nf-core / eager

Open

Competitive mapping for strain separation

3

EisenRa commented Jul 18, 2018

In some metagenomic contexts, there can be closely related species in a sample that can make read mapping to a single reference genome difficult (e.g. cross-mapping of reads between species). In this situation, it can be useful to employ competitive mapping, whereby reference genomes from closely related species are concatenated (in a multifasta), and the reads mapped to this reference. This can a

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