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Projects in Awesome Lists tagged with genomics

A curated list of projects in awesome lists tagged with genomics .

https://github.com/biopython/biopython

Official git repository for Biopython (originally converted from CVS)

bioinformatics biopython dna genomics phylogenetics protein protein-structure python sequence-alignment

Last synced: 16 Dec 2024

https://github.com/google/deepvariant

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

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

Last synced: 17 Dec 2024

https://github.com/lh3/minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

bioinformatics genomics sequence-alignment spliced-alignment

Last synced: 17 Dec 2024

https://github.com/broadinstitute/gatk

Official code repository for GATK versions 4 and up

bioinformatics dna gatk genome genomics ngs science sequencing spark

Last synced: 17 Dec 2024

https://github.com/lh3/bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

bioinformatics fm-index genomics sequence-alignment

Last synced: 17 Dec 2024

https://github.com/greenelab/deep-review

A collaboratively written review paper on deep learning, genomics, and precision medicine

deep-learning genomics manubot manuscript neural-networks review

Last synced: 01 Dec 2024

https://greenelab.github.io/deep-review/

A collaboratively written review paper on deep learning, genomics, and precision medicine

deep-learning genomics manubot manuscript neural-networks review

Last synced: 27 Oct 2024

https://github.com/vgteam/vg

tools for working with genome variation graphs

dna genome-graph genomics graph variation-graph

Last synced: 19 Dec 2024

https://github.com/bigdatagenomics/adam

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

avro big-data bioinformatics genomics java parquet python r scala spark

Last synced: 16 Dec 2024

https://github.com/hail-is/hail

Cloud-native genomic dataframes and batch computing

bioinformatics genetics genomics gwas hail python software vcf

Last synced: 17 Dec 2024

https://github.com/kblin/ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

bioinformatics biology command-line download-genomes genbank genomics ncbi python

Last synced: 01 Nov 2024

https://github.com/google/nucleus

Python and C++ code for reading and writing genomics data.

bioinformatics dna genomics tensorflow

Last synced: 26 Sep 2024

https://github.com/tanghaibao/jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics

allmaps assembly bioinformatics blast comparative-genomics genetic-maps genome-sequencing genomics sequence-alignments synteny variant-calling

Last synced: 19 Dec 2024

https://github.com/BenLangmead/bowtie2

A fast and sensitive gapped read aligner

bioinformatics c-plus-plus genomics read-aligners

Last synced: 13 Nov 2024

https://github.com/deeptools/deepTools

Tools to process and analyze deep sequencing data.

bioinformatics chip-seq genomics ngs python rna-seq

Last synced: 09 Nov 2024

https://github.com/hazyresearch/hyena-dna

Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena

foundation-models genomics language-models

Last synced: 15 Dec 2024

https://github.com/vcflib/vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

genomics genotyping haplotypecaller variant-calling vcf-manipulation

Last synced: 26 Oct 2024

https://github.com/ekg/vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

genomics genotyping haplotypecaller variant-calling vcf-manipulation

Last synced: 30 Oct 2024

https://github.com/voutcn/megahit

Ultra-fast and memory-efficient (meta-)genome assembler

bioinformatics data-structures genome-assembly genomics metagenomics succinct

Last synced: 15 Nov 2024

https://github.com/chhylp123/hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

bioinformatics denovo-assembly genomics hifi-read pacbio

Last synced: 13 Nov 2024

https://github.com/nanoporetech/dorado

Oxford Nanopore's Basecaller

basecalling genomics libtorch nanopore

Last synced: 13 Nov 2024

https://github.com/gmod/jbrowse

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.

bioinformatics biology genome-annotation genome-browser genomics protein-annotation

Last synced: 21 Dec 2024

https://github.com/GMOD/jbrowse

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.

bioinformatics biology genome-annotation genome-browser genomics protein-annotation

Last synced: 01 Nov 2024

https://github.com/mdshw5/pyfaidx

Efficient pythonic random access to fasta subsequences

bgzf bioinformatics dna fasta genomics indexing protein python samtools

Last synced: 17 Dec 2024

https://github.com/poisonalien/maftools

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

bioinformatics cancer-genome-atlas cancer-genomics genomics maf-files r tcga

Last synced: 19 Dec 2024

https://github.com/lucidrains/enformer-pytorch

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

artificial-intelligence attention-mechanism deep-learning dna-sequences gene-expression genomics transformer

Last synced: 19 Dec 2024

https://github.com/instadeepai/nucleotide-transformer

🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

deep-learning dna genomics language-model nucleotide transformer

Last synced: 01 Nov 2024

https://github.com/illumina/hap.py

Haplotype VCF comparison tools

bioinformatics genomics vcf vcf-comparison

Last synced: 21 Dec 2024

https://github.com/nf-core/sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

annotation bioinformatics cancer conda containers gatk4 genomics germline next-generation-sequencing nextflow nf-core pipeline pre-processing reproducible-research somatic target-panels variant-calling whole-exome-sequencing whole-genome-sequencing workflow

Last synced: 07 Nov 2024

https://github.com/lh3/minigraph

Sequence-to-graph mapper and graph generator

bioinformatics genome-graph genomics pan-genome sequence-alignment

Last synced: 15 Dec 2024

https://github.com/aidenlab/juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

3d-genome 3d-genome-browser bioinformatics genomics hi-c ngs

Last synced: 29 Oct 2024

https://github.com/pinellolab/dna-diffusion

🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨

deep-learning diffusion-models diffusion-probabilistic-models generative-model genomics regulatory-genomics stable-diffusion

Last synced: 16 Dec 2024

https://github.com/arvados/arvados

An open source platform for managing and analyzing biomedical big data

arvados aws azure bigdata bioinformatics cloud cluster cwl docker gcp genomics go python ruby workflow workflow-engine

Last synced: 20 Dec 2024

https://github.com/brentp/vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

annotation bioinformatics genomics vcf

Last synced: 18 Dec 2024

https://github.com/brentp/cyvcf2

cython + htslib == fast VCF and BCF processing

bioinformatics cython genomics htslib vcf

Last synced: 17 Nov 2024

https://github.com/higlass/higlass

Fast, flexible and extensible genome browser.

gehlenborglab genomics hi-c higlass visualization

Last synced: 17 Dec 2024

https://github.com/lh3/miniasm

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

bioinformatics denovo-assembly genomics

Last synced: 17 Nov 2024

https://github.com/bedops/bedops

:microscope: BEDOPS: high-performance genomic feature operations

bed bedops bioinformatics c c-plus-plus compression conversion genomics parallel pipeline set set-theory toolkit

Last synced: 14 Nov 2024

https://github.com/nvidia-genomics-research/genomeworks

SDK for GPU accelerated genome assembly and analysis

alignment cuda genomics gpu mapping nvidia partial-order-alignment poa python-api

Last synced: 21 Dec 2024

https://github.com/NVIDIA-Genomics-Research/GenomeWorks

SDK for GPU accelerated genome assembly and analysis

alignment cuda genomics gpu mapping nvidia partial-order-alignment poa python-api

Last synced: 15 Nov 2024

https://github.com/samtools/htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

bam cram dna fasta genomics java java-api ngs sam sequencing vcf

Last synced: 18 Dec 2024

https://github.com/wurmlab/sequenceserver

Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)

bioinformatics blast genomics genomics-visualization hacktoberfest javascript ruby sequence-alignment sequencing visualization

Last synced: 17 Dec 2024

https://github.com/projectglow/glow

An open-source toolkit for large-scale genomic analysis

delta genomics gwas machine-learning population-genetics regression spark

Last synced: 25 Nov 2024

https://github.com/marianattestad/ribbon

A genome browser designed for complex structural variants and long reads.

bioinformatics genome genomics visualization

Last synced: 16 Dec 2024

https://github.com/lh3/wgsim

Reads simulator

bioinformatics genomics

Last synced: 17 Nov 2024

https://github.com/brentp/somalier

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

bioinformatics cancer-genomics genomics

Last synced: 17 Nov 2024

https://github.com/BenLangmead/bowtie

An ultrafast memory-efficient short read aligner

bioinformatics c-plus-plus genomics read-aligners

Last synced: 26 Oct 2024

https://kundajelab.github.io/dragonn/

A toolkit to learn how to model and interpret regulatory sequence data using deep learning.

deep-learning genomics

Last synced: 16 Nov 2024

https://github.com/brentp/slivar

genetic variant expressions, annotation, and filtering for great good.

genomics rare-disease rare-variant-analysis variant-analysis variant-interpretation

Last synced: 17 Nov 2024

https://github.com/KamilSJaron/smudgeplot

Inference of ploidy and heterozygosity structure using whole genome sequencing data

bioinformatics genomics kmer

Last synced: 28 Nov 2024

https://github.com/brentp/smoove

structural variant calling and genotyping with existing tools, but, smoothly.

genomics lumpy structural-variation

Last synced: 21 Dec 2024

https://github.com/deeptools/HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

bioinformatics chromosome-conformation-capture galaxy genomics hic python

Last synced: 09 Nov 2024

https://linsalrob.github.io/ComputationalGenomicsManual/

Robs manual for the computational genomics and bioinformatics class.

bioinformatics genomics online-class

Last synced: 13 Nov 2024

https://github.com/brentp/goleft

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

bioinformatics coverage depth genomics golang

Last synced: 21 Dec 2024

https://github.com/gmod/jbrowse-components

Source code for JBrowse 2, a modern React-based genome browser

bioinformatics genomics jbrowse visualization

Last synced: 20 Dec 2024

https://github.com/lh3/gfatools

Tools for manipulating sequence graphs in the GFA and rGFA formats

bioinformatics genome-graph genomics

Last synced: 17 Nov 2024

https://github.com/haowenz/chromap

Fast alignment and preprocessing of chromatin profiles

bioinformatics chromatin-profiles genomics sequence-analysis

Last synced: 16 Nov 2024

https://github.com/mahmoodlab/porpoise

Pan-Cancer Integrative Histology-Genomic Analysis via Multimodal Deep Learning - Cancer Cell

genomics histology mahmoodlab pan-cancer-analysis wsi-images

Last synced: 20 Dec 2024

https://github.com/mahmoodlab/mcat

Multimodal Co-Attention Transformer for Survival Prediction in Gigapixel Whole Slide Images - ICCV 2021

early-fusion genomics mahmoodlab mcat multimodal multimodal-deep-learning multimodal-fusion pathology

Last synced: 20 Dec 2024

https://github.com/LooseLab/readfish

CLI tool for flexible and fast adaptive sampling on ONT sequencers

adaptive-sampling bioinformatics genomics ont oxford-nanopore sequencing

Last synced: 13 Nov 2024

https://github.com/bioinform/neusomatic

NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection

convolutional-neural-networks deep-learning genomics somatic-variants

Last synced: 16 Nov 2024

https://github.com/lh3/kmer-cnt

Code examples of fast and simple k-mer counters for tutorial purposes

bioinformatics genomics k-mer-counting

Last synced: 17 Nov 2024

https://github.com/lh3/cgranges

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

algorithm bioinformatics genomics

Last synced: 19 Dec 2024

https://github.com/mlin/GenomicSQLite

Genomics Extension for SQLite

bioinformatics genomics sequencing sqlite sqlite3

Last synced: 19 Nov 2024

https://github.com/mahmoodlab/MCAT

Multimodal Co-Attention Transformer for Survival Prediction in Gigapixel Whole Slide Images - ICCV 2021

early-fusion genomics mahmoodlab mcat multimodal multimodal-deep-learning multimodal-fusion pathology

Last synced: 13 Nov 2024

https://github.com/mlin/genomicsqlite

Genomics Extension for SQLite

bioinformatics genomics sequencing sqlite sqlite3

Last synced: 15 Dec 2024

https://github.com/stephenturner/qqman

An R package for creating Q-Q and manhattan plots from GWAS results

cran genomics gwas r

Last synced: 18 Dec 2024

https://github.com/lh3/psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

bioinformatics genomics population-genetics

Last synced: 17 Nov 2024

https://github.com/brentp/hts-nim

nim wrapper for htslib for parsing genomics data files

bioinformatics genomics high-throughput-sequencing htslib nim nim-lang

Last synced: 17 Nov 2024

https://github.com/divonlan/genozip

A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too

23andme bam bgzip bwa compression cram fasta fastq genomics gvf gzip sam samtools vcf

Last synced: 13 Nov 2024

https://github.com/brentp/echtvar

using all the bits for echt rapid variant annotation and filtering

genetic-variants genomics variant-analysis variant-annotations

Last synced: 15 Dec 2024

https://github.com/goekelab/xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing

genomics machine-learning modification nanopore nanopore-sequencing python rna rna-modifications rna-seq transcriptomics

Last synced: 16 Dec 2024

https://github.com/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 download genbank genome genomes genomics ncbi refseq sequence

Last synced: 07 Nov 2024

https://github.com/AdmiralenOla/Scoary

Pan-genome wide association studies

bacteria gene-presence-absence genomics gwas pan-genome

Last synced: 03 Nov 2024

https://github.com/GoekeLab/xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing

genomics machine-learning modification nanopore nanopore-sequencing python rna rna-modifications rna-seq transcriptomics

Last synced: 13 Nov 2024

https://github.com/marianattestad/assemblytics

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

assembly bioinformatics genomics

Last synced: 30 Oct 2024

https://github.com/brentp/peddy

genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF

ancestry bioinformatics genomics genotype pedigree vcf

Last synced: 20 Dec 2024