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Search results for sequencing ngs

94 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.

Fastp ⭐ 1,602

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging.

Official code repository for GATK versions 4 and up

Galaxy ⭐ 1,211

Data intensive science for everyone.

Tools for working with genomic and high throughput sequencing data.

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

Sortmerna ⭐ 220

SortMeRNA: next-generation sequence filtering and alignment tool

UGENE is free open-source cross-platform bioinformatics software

Afterqc ⭐ 157

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

Ngstools ⭐ 142

Programs to analyse NGS data for population genetics purposes

Sequana ⭐ 136

Sequana: a set of Snakemake NGS pipelines

Seq2science ⭐ 132

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

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

Crispresso ⭐ 110

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data

Ngscheckmate ⭐ 106

Software program for checking sample matching for NGS data

Gencore ⭐ 103

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

Accurate and flexible loops calling tool for 3D genomic data.

🚀 seqfu - Sequece Fastx Utilities

Ngs Pipe ⭐ 87

NGS-pipe: next-generation sequencing pipelines for precision oncology

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.

Opengene.jl ⭐ 61

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

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.

Community_software_tools_for_ngs ⭐ 46

Grabseqs ⭐ 44

A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA

Snpsplit ⭐ 43

Allele-specific alignment sorting

A RepSeq processing swiss-knife

Needlestack ⭐ 39

Multi-sample somatic variant caller

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

Ngstools ⭐ 37

Next-Generation Sequencing(NGS) toolkits.

Mapdamage ⭐ 37

mapDamage: tracking and quantifying damage patterns in ancient DNA sequences

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.

Seqcluster ⭐ 34

small RNA analysis from NGS data

Moved to: https://github.com/maxplanck-ie/parkour2

Uniquekmer ⭐ 33

Generate unique KMERs for every contig in a FASTA file

Hpg Aligner ⭐ 32

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

Bio Dockers ⭐ 32

🐳 Bio-dockers: dockerized bioinformatic tools

Fastq_utils ⭐ 29

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

Bac Genomics Scripts ⭐ 28

Collection of scripts for bacterial genomics

Ngs Filters ⭐ 25

Filters for false-positive mutation calls in NGS

Ctdna Pipeline ⭐ 24

A simplified pipeline for ctDNA sequencing data analysis

Ngstools ⭐ 23

My own tools code for NGS data analysis (Next Generation Sequencing)

Bioinf2019 ⭐ 23

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

Flexible Genotyping of Polyploids using Next Generation Sequencing Data

Seqmaker.jl ⭐ 19

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

Gatk4_best_practice ⭐ 18

GATK4 Best Practice Nextflow Pipeline

Sequenceng ⭐ 18

An interactive learning resource for next-generation sequencing (NGS) techniques

Nanovar Archived ⭐ 17

Archived version 1.0.2

Next generation sequencing (NGS/HTS) tools.

Copenhagen ⭐ 17

Analysis of genotyping and next-generation sequencing data in medical and population genetics

Ctdnatools ⭐ 17

R package to work with ctDNA sequencing data

A toolkit developed by JhuangLab members to facilitate the analysis of next-generation sequencing (NGS) data.

k-mer based Pipeline to identify the Serotype from Illumina NGS reads

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

Angsd Wrapper ⭐ 13

Utilities for analyzing next generation sequencing data.

Prophage_tracer ⭐ 13

Prophage Tracer: precisely tracing prophages in prokaryotic genomes using overlapping split-read alignment

Manuscript describing ChronQC is now available online in Bioinformatics

CAVA (Clinical Annotation of VAriants)

Ngs Pipeline ⭐ 12

Pipeline for Somatic Variant Calling with WES and WGS data

Groovy Ngs Utils ⭐ 12

A collection of utilities for working with next generation (MPS) sequencing data in Groovy

less like viewer for fastq files

Deepvariant On Spark ⭐ 11

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

Normalization and difference calling for Next Generation Sequencing (NGS) data via joint multinomial modeling.

Ngsderive ⭐ 10

Forensic analysis tool useful in backwards computing information from next-generation sequencing data.

Banzai Microbialgenomics Pipeline ⭐ 10

Banzai is a Microbial Genomics Next Generation Sequencing (NGS) Pipeline Tool developed within Dr Scott Beatson’s Group at the University of Queensland

Next-Generation Sequencing (NGS) Data Processing Tool & Library

Ngsparalog ⭐ 9

Copy number variation detection using NGS data.

Star Seqr ⭐ 9

RNA Fusion Detection and Quantification

An integrated analysis toolkit and pipeline for Next-Generation Sequencing (NGS) panel sequencing data

Auto_process_ngs ⭐ 8

Scripts and utilities for automatic processing & management of Illumina NGS sequencing data.

Trumicount ⭐ 8

Correctly counting molecules using unique molecular identifiers (UMIs)

Ngs Workflows ⭐ 8

Source code, data and documentation to demonstrate automation in NGS data analysis

Ngs580 Nf ⭐ 7

Target exome sequencing analysis for NYU NGS580 gene panel

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

Biotech7005 ⭐ 7

The practical material from the course Biotech 7005: Bioinformatics and Systems Modelling

HTSinfer infers metadata from Illumina high throughput sequencing (HTS) data

Next-generation sequencing analysis pipelines & scrips

Transgener ⭐ 6

Transgene integration and rearrangement discovery using NGS

Onlineadapterdatabase ⭐ 6

Linking publicly deposited data to sequencing adapters.

Filters for Next Generation Sequencing

Appliedgenomeresearch ⭐ 6

course about NGS data processing: genomics and transcriptomics

a tool for predicting mitochondrial DNA deletions using soft-clipping

QC checks and metrics for Illumina NGS data

Bsfpython ⭐ 5

A Python library to manage day-to-day analysis of next generation sequencing (NGS) data by the Biomedical Sequencing Facility (BSF).

Mutationseq ⭐ 5

Software for somatic SNV detection using next generation sequencing (NGS) data.

Decontaminer ⭐ 5

DecontaMiner is a tool designed and developed to investigate the presence of contaminating sequences in unmapped NGS data. It can suggest the presence of contaminating organisms in sequenced samples, that might derive either from laboratory contamination or from their biological source, and in both cases can be considered as worthy of further investigation and experimental validation. The novelty of DecontaMiner is mainly represented by its easy integration with the standard procedures of NGS da

Fastq To Bam ⭐ 5

Optimised pipeline to process whole genome sequence data from fastq to BAM on NCI Gadi

Cirrus Ngs ⭐ 5

Automated Pipeline for Variant/Haplotype Calling and Filtering

Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculations

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