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218 search results found

Deepvariant ⭐ 2,978

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

Official code repository for GATK versions 4 and up

Nextstrain build for novel coronavirus SARS-CoV-2

Mosdepth ⭐ 617

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

Sniffles ⭐ 479

Structural variation caller using third generation sequencing

Graph-based alignment (Hierarchical Graph FM index)

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

Crispresso2 ⭐ 233

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

Rapid large-scale prokaryote pan genome analysis

Smudgeplot ⭐ 200

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Soapdenovo2 ⭐ 197

Next generation sequencing reads de novo assembler.

Circlator ⭐ 193

A tool to circularize genome assemblies

Artemis ⭐ 191

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

Kubegene ⭐ 169

KubeGene - A turn-key Genome Sequencing workflow management framework

Insilicoseq ⭐ 158

🚀 A sequencing simulator

Nextpolish ⭐ 145

Fast and accurately polish the genome generated by long reads.

Genomescope ⭐ 135

Fast genome analysis from unassembled short reads

Rnaseq Workflow ⭐ 133

A repository for setting up a RNAseq workflow

Dna Seq Analysis ⭐ 128

DNA sequencing analysis notes from Ming Tang

Mirdeep2 ⭐ 120

Discovering known and novel miRNAs from small RNA sequencing data

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

Canvas - Copy number variant (CNV) calling from DNA sequencing data

A handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.

Finch Rs ⭐ 87

A genomic minhashing implementation in Rust

Fast and memory-efficient sequencing error corrector

Parliament2 ⭐ 83

Runs a combination of tools to generate structural variant calls on whole-genome sequencing data

Mcclintock ⭐ 83

Meta-pipeline to identify transposable element insertions using next generation sequencing data

Making whole bacterial genome sequencing data analysis easy

An R package for performing STAAR procedure in whole-genome sequencing studies

Sv Cnv Studies ⭐ 81

📚 Relevant papers for CNV and SV approaches

Deepsimulator ⭐ 76

The first deep learning based Nanopore simulator which can simulate the process of Nanopore sequencing.

Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)

Ichorcna ⭐ 73

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

Neoantigen Vaccine Pipeline ⭐ 72

Bioinformatics pipeline for selecting patient-specific cancer neoantigen vaccines

Smrnaseq ⭐ 63

A small-RNA sequencing analysis pipeline

SV caller for nanopore data

A package for designing compact and comprehensive capture probe sets.

The genome assembler that reduces the computational time of human genome assembly from 400,000 CPU hours to 2,000 CPU hours, utilizing long erroneous 3GS sequencing reads and short accurate NGS sequencing reads.

An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.

Method for detecting STR expansions from short-read sequencing data

Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.

Bioinformatics_notes ⭐ 52

Bioinformatics and genomics resources

Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data

Visualization and annotation of CNVs from population-scale whole-genome sequencing data

reference-guided aligner for next-generation sequencing technologies

Appliedgenomics2017 ⭐ 49

JHU EN.600.649: Computational Genomics: Applied Comparative Genomics

Svim Asm ⭐ 48

Structural Variant Identification Method using Genome Assemblies

MARVEL: Metagenomic Analyses and Retrieval of Viral ELements

Pipeline Standardization ⭐ 47

Shatterseek ⭐ 46

Deepsomatic ⭐ 45

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

Cloud-based single-cell copy-number variation analysis tool

Ncov Tools ⭐ 44

Small collection of tools for performing quality control on coronavirus sequencing data and genomes

Genome guided re-segmention and visualization for raw nanopore sequencing data.

Physalia Lcwgs ⭐ 43

Files for the the Physalia course on Population genomic inference from low-coverage whole-genome sequencing data, Oct 10-13, 2022

Snpsplit ⭐ 43

Allele-specific alignment sorting

Fluentdna ⭐ 43

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

Platinumgenomes ⭐ 42

The Platinum Genomes Truthset

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

Isaac_variant_caller ⭐ 38

This project is deprecated, please see strelka2 at https://github.com/Illumina/strelka

10x Genomics Reads Simulator

Cnvcaller ⭐ 37

parallelized blat with multi-threads support

DNAscan is a fast and efficient bioinformatics pipeline that allows for the analysis of DNA Next Generation sequencing data, requiring very little computational effort and memory usage.

Genome Data Integration ⭐ 35

Methods to integrate data from multiple genome sequencing datasets and form consensus variant calls

Ploidyngs ⭐ 35

Explore ploidy levels from NGS data alone

Data_science_in_biology ⭐ 35

projects using galaxy, python, linux command line to analyze sequencing data

QDNAseq package for Bioconductor

Uniquekmer ⭐ 33

Generate unique KMERs for every contig in a FASTA file

Mitofinder ⭐ 32

MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data

Fast and accurate tool for estimating genomic distances between genome-skims

Nano Snakemake ⭐ 31

A snakemake pipeline for SV analysis from nanopore genome sequencing

Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity

Full-spectrum copy number variation detection by high-throughput DNA sequencing

Treetoreads ⭐ 29

Pipeline to generate NGS reads from a phylogeny

Shallowhrd ⭐ 28

This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination Deficiency of a tumor based on the number of Large-scale Genomic Alterations (LGAs).

Enhanced Artificial Genome Engine: next generation sequencing reads simulator

RNASeq pipeline

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

Data and information about the Polaris study

Deepstats ⭐ 27

deepStats: a stastitical toolbox for deeptools and genomic signals

an empirical Bayesian framework for mutation detection from cancer genome sequencing data

Awesome Sequencing Tech Papers ⭐ 26

A collection of publications on comparison of high-throughput sequencing technologies.

Igenomics ⭐ 26

The first app for Mobile DNA Sequence Alignment and Analysis

TELR is a fast non-reference transposable element detector from long read sequencing data.

Pathoscope ⭐ 25

Pathoscope: Species identification and strain attribution with unassembled sequencing data

Readdepth ⭐ 24

R package for inferring copy number from read depth

Dna Me Pipeline ⭐ 24

DCC/DAC methylation pipeline source

Long Read Catalog ⭐ 23

catalog for long-read sequencing tools

Bioinformatics Course 2020 ⭐ 23

gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (WGBS).

A genomics pipeline build on top of the GATK Queue framework. Main repository: https://github.com/NationalGenomicsInfrastructure/ (make sure you fork from there)

Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝

Aceseqworkflow ⭐ 22

Allele-specific copy number estimation with whole genome sequencing

Giab_tools_methods ⭐ 22

This repository contains a list of tools or methods that have been used in GIAB analysis

mBin: a methylation-based binning framework for metagenomic SMRT sequencing reads

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1-100 of 218 search results

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