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91 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

Galaxy ⭐ 1,211

Data intensive science for everyone.

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

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads

Comp Genomics Class ⭐ 236

Code and examples for JHU Computational Genomics class

pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)

UGENE is free open-source cross-platform bioinformatics software

Nextclade ⭐ 190

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

Genomics ⭐ 154

A collection of scripts and notes related to genomics and bioinformatics

Tcga_example ⭐ 135

Dna Seq Analysis ⭐ 128

DNA sequencing analysis notes from Ming Tang

Dnanalyzer ⭐ 122

Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools

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

Optitype ⭐ 106

Precision HLA typing from next-generation sequencing data

Fastq.bio ⭐ 93

An interactive web tool for quality control of DNA sequencing data

Ichorcna ⭐ 73

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

Reseqtools ⭐ 68

A Toolkit for analyzing next-generation DNA Re-Sequencing data

Methpipe ⭐ 63

A pipeline for analyzing DNA methylation data from bisulfite sequencing.

A package for designing compact and comprehensive capture probe sets.

Tumor Heterogeneity Analysis (THetA) and THetA2 are algorithms that estimate the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data. This repository includes the updated algorithm, called THetA2.

Nanocall ⭐ 61

An Oxford Nanopore Basecaller

Atac Seq ⭐ 51

Exomedepth ⭐ 46

ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.

Deepsomatic ⭐ 45

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

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.

Dna Methylation Analysis ⭐ 42

DNA methylation analysis notes from Ming Tang

Mapdamage ⭐ 37

mapDamage: tracking and quantifying damage patterns in ancient DNA sequences

Data_science_in_biology ⭐ 35

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

Hlatyping ⭐ 34

Precision HLA typing from next-generation sequencing data

QDNAseq package for Bioconductor

Hpg Aligner ⭐ 32

HPG Aligner is an ultrafast and highly sensitive Next-Generation Sequencing (NGS) mapper which supoprts both DNA and RNA alignment

Algorithms Dna Sequencing ⭐ 26

🧬 Algorithms for DNA Sequencing by Johns Hopkins University

NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data

Igenomics ⭐ 26

The first app for Mobile DNA Sequence Alignment and Analysis

Primavera ⭐ 25

🌸 Python library for primer-based verification of DNA assemblies: primer selection, data analyis, etc.

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

Clinical DNA Sequencing Analysis and Data Warehouse

PathOS is a clinical application for filtering, analysing and reporting on NGS variants

Amrplusplus_v2 ⭐ 21

MEGARes and AmrPlusPlus - A comprehensive database of antimicrobial resistance genes and user-friendly pipeline for analysis of high-throughput sequencing data

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

Gargammel ⭐ 20

gargammel is an ancient DNA simulator

Methylcc ⭐ 20

R/BioC package to estimate the cell composition of whole blood in DNA methylation samples in microarray or sequencing platforms

Ctdnatools ⭐ 17

R package to work with ctDNA sequencing data

Scdna_myeloid ⭐ 16

Processing scripts for single cell DNA sequencing on the Tapestri platform

Kineticstools ⭐ 16

Tools for detecting DNA modifications from single molecule, real-time sequencing data

Structural Variation and fusion detection using targeted sequencing data from circulating cell free DNA

Distribution Based Clustering ⭐ 14

Extremely accurate algorithm used to group DNA sequences from microbial communities into operational taxonomic units (proxy for species) for ecological or biomedical research. This algorithm uses the information contained in the distribution of DNA sequences across samples along with sequence similarity to cluster sequences more accurately than other methods that are currently available. Developed for Illumina next-generation sequencing libraries, but applicable to any sequencing platform with s

Almostsignificant ⭐ 13

A server for maintaining high-throughput sequencing QC data

NGS DNA best practice pipeline for Illumina sequencing - alignment, variant calling, annotation and QC

About_giab ⭐ 13

An introduction about the Genome-in-a-Bottle project

An HLA star-calling tool for PacBio HiFi data types

Materials presented at the BiocNYC meet-up

Deepvariant On Spark ⭐ 11

DeepVariant-on-Spark is a germline short variant calling pipeline that runs Google DeepVariant on Apache Spark at scale.

MethGo: a comprehensive tool for analyzing whole-genome bisulfite sequencing data

Illumina analysis pipeline

Nucleosome_ctdna ⭐ 11

Inferring expressed genes by whole-genome sequencing of plasma DNA

Sequencing_for_genetics ⭐ 11

유전학자를 위한 시퀀싱 자료 분석

Single-cell COPy number Estimation

Methtuple ⭐ 10

methtuple is a methylation caller for methylation events that co-occur on the same DNA fragment from high-throughput bisulfite sequencing data, such as methylC-seq.

Haplotyped Methylome ⭐ 10

Reproducibility workflow for Gigante et al., 2018: Using long-read sequencing to detect imprinted DNA methylation

Matchclips2 ⭐ 9

paired end distance, split reads matching, read depth are used to detect and precisely locate structure variations

Sequencing to the people!

Ascii_dna_translator ⭐ 9

DNA as an information storage medium using either 4-base codon or binary representations of 256-ASCII

Biogrinder ⭐ 9

Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.

A Coupled-Clone Nonnegative Matrix Factorization Method for Integrating Tumor Single-Cell RNA and DNA Sequencing Data

Dnaseq_pipeline ⭐ 8

Pipeline in place at the UGI for DNA level analysis

Fastq.bio Serverless ⭐ 7

An interactive web tool for quality control of DNA sequencing data, using Cloudflare workers running WebAssembly

Fonda is a framework which offers scalable and automatic analysis of multiple NGS sequencing data types

PuntSeq - Chasing the microbial diversity of Cambridge's freshwater

Polonator ⭐ 7

DNA sequencing device controller software

Somatic Mutation Calling Using Both DNA and RNAseq Data

Mean Alterations Using Discrete Expression

Biocode Lims ⭐ 7

The Biocode LIMS plugin integrates Geneious with your lab workflow, allowing you to track processes through tissue sample, extraction, PCR, sequencing and assembly. It is best suited for large scale DNA barcoding efforts.

Pseudoseq.jl ⭐ 6

Fake genomes, fake sequencing, real insights.

Schloss_pacbio16s_peerj_2016 ⭐ 6

Repo for Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system

Methylation_notes ⭐ 6

Notes on DNA methylation analysis

Fast5tools ⭐ 6

Tools for working with fast5 files (nanopore data).

Monsterlab ⭐ 6

Monster Lab: teaching the science of sequencing with Lego

Cell Free Dna Reading List ⭐ 6

Important papers relating to the biology of cell free DNA

A graph-based genotyper for aligned DNA sequencing data

A comprehensive, accurate and efficient solution for analysis of large scale base-resolution DNA methylation data

Tracetuner ⭐ 5

TraceTuner, the DNA sequencing quality value, base calling and trace processing software.

Bioinformatic software for TAPS DNA methylation sequencing

Algorithms For Dna Sequencing ⭐ 5

Coursera MOOC Algorithms for DNA Sequencing by Ben Langmead, PhD, Jacob Pritt

Ancient DNA Read Simulator for Metagenomic

Schloss_pacbio16s_peerj_2015 ⭐ 5

Repository to accompany "Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system"

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