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504 search results found

Fastq.bio ⭐ 93

An interactive web tool for quality control of DNA sequencing data

Bwa Meme ⭐ 92

BWA-MEME: Faster BWA-MEM2 using learned-index

Assembly Stats ⭐ 92

Get assembly statistics from FASTA and FASTQ files

Dolphinnext ⭐ 92

A graphical user interface for distributed data processing of high throughput genomics

Fermikit ⭐ 91

De novo assembly based variant calling pipeline for Illumina short reads

Earlgrey ⭐ 90

Earl Grey: A fully automated TE curation and annotation pipeline

Genomicsdb ⭐ 88

High performance data storage for importing, querying and transforming variants.

A DNA Sequence Alignment/Map (SAM) library for Clojure

Mccortex ⭐ 86

De novo genome assembly and multisample variant calling

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

Framework for building fast genomics web tools with WebAssembly and WebWorkers

Awesome 10x Genomics ⭐ 81

List of tools and resources related to the 10x Genomics GEMCode/Chromium system

Genomicdatacommons ⭐ 80

Provide R access to the NCI Genomic Data Commons portal.

Tiledb Vcf ⭐ 79

Efficient variant-call data storage and retrieval library using the TileDB storage library.

Comparative Genomics Toolkit 3

Bayesian genotyper for structural variants

Genomics ⭐ 78

Scripts, utilities and programs for genomic bioinformatics.

R Bioinformatics Cookbook ⭐ 76

R Bioinformatics Cookbook, published by Packt

Flexible genotype query among 30,000+ samples whole-genome

Callings Nf ⭐ 76

GATK RNA-Seq Variant Calling in Nextflow

Fast hash function for DNA/RNA sequences

OhmNet: Representation learning in multi-layer graphs

Czid Web ⭐ 75

Infectious Disease Sequencing Platform

Toolkit for calling structural variants using short or long reads

Grep for FASTQ files

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

Python package and CLI for whole-genome duplication related analyses

Extensible specification for representing and uniquely identifying biological sequence variation

Geoquery ⭐ 73

The bridge between the NCBI Gene Expression Omnibus and Bioconductor

EDGE is a highly adaptable bioinformatics platform that allows laboratories to quickly analyze and interpret genomic sequence data.

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

A WGS de novo assembler based on the FMD-index for large genomes

A Python-based Effective Feature Generation Tool from DNA, RNA, and Protein Sequences

Fermi Lite ⭐ 67

Standalone C library for assembling Illumina short reads in small regions

Geneticsmakie.jl ⭐ 66

🧬High-performance genetics- and genomics-related data visualization using Makie.jl

Coolpuppy ⭐ 66

A versatile tool to perform pile-up analysis on Hi-C data in .cool format.

Merging, Annotation, Validation, and Illustration of Structural variants

Dna Traits ⭐ 64

A fast 23andMe genome text file parser, now superseded by arv

A package for designing compact and comprehensive capture probe sets.

Cut Runtools 2.0 ⭐ 62

CUT&RUN and CUT&Tag data processing and analysis

Awesome Genetics ⭐ 62

A curated list of awesome bioinformatics software.

Gatb Core ⭐ 61

Core library of the Genome Analysis Toolbox with de-Bruijn graph

Pax_sapientica ⭐ 61

🌿: GIS for philological, archaeological, and anthropological data.

Splitthreader ⭐ 60

Explore rearrangements and copy-number amplifications in a cancer genome

Mungesumstats ⭐ 59

Rapid standardisation and quality control of GWAS or QTL summary statistics

High-performance error correction for Illumina resequencing data

🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes

Palimpsest ⭐ 56

An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.

Simplesam ⭐ 55

Simple pure Python SAM parser and objects for working with SAM records

Command line utility for manipulating Illumina-generated FASTQ files.

Awesome Structural Bioinformatics ⭐ 54

Structural Bioinformatics is awesome. Throw your textbook in the garbage, light the garbage can on fire, and blend the ashes into your cold brew almond milk latte and read this.

Arioc: GPU-accelerated DNA short-read alignment

Microbetrace ⭐ 53

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

Trackplot ⭐ 52

trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets.

Bioinformatics_notes ⭐ 52

Bioinformatics and genomics resources

Geneview ⭐ 51

Genomics data visualization in Python by using matplotlib.

Model and predict short DNA sequence features with neural networks

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

Graph-based mapping of long sequences, noisy or HiFi.

Teamteri ⭐ 50

Genomics (computational bioinformatic data analysis) running on GCP, AWS or Azure

A fork of minimap2 optimized for assembly-to-reference alignment

Appliedgenomics2017 ⭐ 49

JHU EN.600.649: Computational Genomics: Applied Comparative Genomics

vcfdist: Accurately benchmarking phased variant calls

Predict AMPs in (meta)genomes and peptides

Htstream ⭐ 48

A high throughput sequence read toolset using a streaming approach facilitated by Linux pipes

Full_spectrum_bioinformatics ⭐ 47

An open-access bioinformatics text

Minimap2 Rs ⭐ 46

Rust bindings to minimap2 library

Python3 scripts to manipulate FASTA and FASTQ files

GEne Cluster prediction with COnditional random fields.

Bio Pipeline ⭐ 45

My collection of light bioinformatics analysis pipelines for specific tasks

Deepsomatic ⭐ 45

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data.

Performs memory-efficient reservoir sampling on very large input files delimited by newlines

Sevenbridges Python ⭐ 44

SevenBridges Python Api bindings

Elucidating the Utility of Genomic Elements with Neural Nets

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

Vrs Python ⭐ 44

GA4GH Variation Representation Python Implementation

a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies

A versatile compressor of third generation sequencing reads.

Phigaro is a scalable command-line tool for predicting phages and prophages

PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.

ClairS - a deep-learning method for long-read somatic small variant calling

Hts Nim Tools ⭐ 41

useful command-line tools written to show-case hts-nim

Pymsaviz ⭐ 41

MSA(Multiple Sequence Alignment) visualization python package for sequence analysis

genEra is a fast and easy-to-use command-line tool that estimates the age of the last common ancestor of protein-coding gene families.

Bystro genetic analysis (annotation, filtering, statistics)

Liblevenshtein Java ⭐ 40

Various utilities regarding Levenshtein transducers. (Java)

Jgi Query ⭐ 40

A simple command-line tool to download data from Joint Genome Institute databases

Balsamic ⭐ 40

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Tomahawk ⭐ 39

Fast calculations of linkage-disequilibrium in large-scale human cohorts

Assembly_improvement ⭐ 39

Improve the quality of a denovo assembly by scaffolding and gap filling

A fast constructor of the compressed de Bruijn graph from many genomes

A fast tool for hybrid genome assembly of long and short reads

Biopython Coronavirus ⭐ 39

Biopython Jupyter Notebook tutorial to characterize a small genome

Rustybam ⭐ 38

bioinformatics toolkit in rust

Aws For Bioinformatics ⭐ 38

AWS for Bioinformatics Researchers

Pathogen Informatics Training ⭐ 38

My experimental tools on top of htslib. NOT OFFICIAL!!!

Dnapipete ⭐ 38

dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X).

Related Searches

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