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Search results for genome ngs

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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

Snakepipes ⭐ 359

Customizable workflows based on snakemake and python for the analysis of NGS data

Ngsplot ⭐ 231

Quick mining and visualization of NGS data by integrating genomic databases

New Genome Browser (NGB) - a Web - based NGS data viewer with unique Structural Variations (SVs) visualization capabilities, high performance, scalability, and cloud data support

Viral Ngs ⭐ 129

Viral genomics analysis pipelines

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

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models

Mcclintock ⭐ 83

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

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

A package for designing compact and comprehensive capture probe sets.

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.

Read Assembly and Annotation Pipeline Tool

A scalable bacterial genome assembly, annotation and analysis pipeline

Snpsplit ⭐ 43

Allele-specific alignment sorting

Ngs Primerplex ⭐ 42

NGS-PrimerPlex is a high-throughput tool for mupltiplex primer design

Ley Lab MetaGenome Profiler DataBase generator

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.

Uniquekmer ⭐ 33

Generate unique KMERs for every contig in a FASTA file

Mtbseq_source ⭐ 32

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

Mindthegap ⭐ 30

MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.

The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline

NGS Data Analysis Textbook Version 2 (Disease Genome Analysis)

VAPiD: Viral Annotation and Identification Pipeline

Comparative_genomics ⭐ 24

Micro 612 genomics workshop

INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomic surveillance

Biokanga ⭐ 22

An integrated high performance bioinformatics toolkit

Kart: A divide-and-conquer algorithm for NGS read mapping with high error tolerance

Rnaseq Nf ⭐ 20

RNAseq analysis pipeline

Seqmaker.jl ⭐ 19

(No maintenance) Next Generation Sequencing Simulation with SNP, Variation and Sequencing Error Integrated

Seqqscorer ⭐ 18

Svcollector ⭐ 17

Method to optimally select samples for validation and resequencing

Nanovar Archived ⭐ 17

Archived version 1.0.2

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

Tracespipe ⭐ 16

Reconstruction and analysis of viral and host genomes at multi-organ level

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

LAVA: Lightweight Assignment of Variant Alleles

bacterial genome annotation system

Rnftools ⭐ 13

RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.

An automated ChIP-seq pipeline using Nextfow

Ngs Handout ⭐ 12

This project is in the process of being ported over to another repository.

CAVA (Clinical Annotation of VAriants)

Ngs_te_mapper ⭐ 9

Software for detecting transposable element insertions from next-generation sequencing data

Xenomapper ⭐ 8

A utility for splitting mixed origin NGS reads

A software to detect virome-wide integrations

Nanosim H ⭐ 8

NanoSim-H: a simulator of Oxford Nanopore reads; a fork of NanoSim.

Nextflow_pipelines ⭐ 8

The set of NGS processing pipelines used at Babraham

Python NGS Repository

Viral Assemble ⭐ 8

viral-ngs: genome assembly and scaffolding

Hpg Methyl ⭐ 7

An ultrafast and highly sensitive Next-Generation Sequencing (NGS) read mapper and methylation extractor.

Estimate NGS Dataset qualitity in terms of its ability to detect mutations of predefined spectrum

Rediscover ⭐ 5

RNA editing discovery from NGS data.

Alienomics ⭐ 5

Automated pipeline for HGT and contaminant detection in an assembled, annotated genome

Ngshmmalign ⭐ 5

ngshmmalign is a profile HMM aligner for NGS reads designed particularly for small genomes (such as those of RNA viruses like HIV-1 and HCV) that experience substantial biological insertions and deletions

Eliminating Assembly Gaps by Long read Extension

Varcall2015 ⭐ 5

Materials for the VarCall2015 course

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