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ngs-pipeline

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flowhub-team /awesome-omics

A collection of awesome things regarding all omics.

awesome genomics ngs protein omics single-cell ngs-pipeline wgs-analysis

UpdatedJan 23, 2024

patidarr /ngs_pipeline

Exome/Capture/RNASeq Pipeline Implementation using snakemake

snakemake pipeline panel ngs tophat gatk rnaseq fastq exome ngs-pipeline annovar snpeff

UpdatedMar 26, 2018
Python

CSBB-Shiny

praneet1988 /CSBB-Shiny

Computational Suite for Bioinformaticians and Biologists (CSBB) is a RShiny application developed with an intention to empower researchers from wet and dry lab to perform downstream Bioinformatics analysis

ngs data-visualization rshiny data-analysis single-cell data-normalization analysis-framework ngs-analysis single-cell-rna-seq ngs-pipeline rshiny-application

UpdatedApr 5, 2023
R

ncbi /pm4ngs

Project Manager for NGS data analysis

bioinformatics next-generation-sequencing rnaseq ngs-analysis ngs-pipeline cwl-workflow chipseq chipexo

UpdatedAug 24, 2022
Python

ncbi /cwl-ngs-workflows-cbb

A set of CWL tools and workflows used by NCBI Computational Biology Branch for NGS data analysis

ngs ngs-analysis ngs-pipeline cwl-workflow

UpdatedJun 29, 2023
Common Workflow Language

viromelab /tracespipe

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

virus pipeline ngs clinical metagenomics forensics virology ngs-pipeline mtdna multi-organ

UpdatedSep 30, 2024
Shell

caulilin /QTG_Seq

bsa ngs-pipeline qtl-analyses fine-mapping

UpdatedJan 11, 2019
R

epigen /open_pipelines

Pipelines for NGS data preprocessing by the Bock lab and friends

bioinformatics rna-seq pipeline chip-seq atac-seq looper ngs-pipeline pypiper

UpdatedAug 29, 2022
Python

nf-cmgg /structural

A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads

annotation repeats ngs cnv cram structural-variation ngs-pipeline nextflow-pipeline short-reads

UpdatedFeb 21, 2025
Nextflow

angelovangel /nxf-fastqc

A simple fastp-MultiQC nextflow pipeline

multiqc fastq-files ngs-pipeline fastqc nextflow-pipelines

UpdatedFeb 2, 2023
Nextflow

jnarayan81 /setu

SARS-CoV-2 Genome Assembler

genome assembler genome-assembly ngs-pipeline covid19 sars-cov-2

UpdatedApr 11, 2023
Shell

hivdb /codfreq

FASTQ-to-CodFreq pipeline for HIV-1 and SARS-CoV-2

hiv ngs-pipeline sars-cov-2

UpdatedMar 21, 2024
Python

NCBI-Hackathons /FlowBio

A fast, easy way to present complex bioinformatics pipelines to biologists

bash docker pipeline nextflow jupyter-notebook pipeline-framework ncbi ngs-pipeline

UpdatedSep 28, 2018
Shell

rusalkaguy /snakemake-slurm-tutorial

Working example of snakemake tutorial using UAB Cheaha computing cluster via SLURM scheduler

snakemake ngs slurm ngs-pipeline

UpdatedNov 8, 2018
Python

Hughes-Genome-Group /NGseqBasic

Mapping, filtering, and data hub visualisation pipeline for DNase, ATAC, ChIP data

UpdatedDec 23, 2019
Shell

nf-core /denovohybrid

UNDER CONSTRUCTION: Hybrid genome assembly pipeline using a combination of long and short sequencing reads

workflow nanopore pipeline nextflow assembly denovo genome-assembly denovo-assembly ngs-pipeline nanopore-sequencing nf-core hybrid-assembly

UpdatedDec 19, 2022
Nextflow

bpucker /yam

scripts associated with yam genome assembly

coverage assembly ngs dna gene-annotation genome-assembly phasing gene-prediction ngs-pipeline busco

UpdatedMay 8, 2020
Python

dmnfarrell /snipgenie

command line and desktop tool for microbial variant calling

python bioinformatics genomics pyqt5 pyside2 variant-calling ngs-pipeline

UpdatedFeb 27, 2025
Jupyter Notebook

nf-cmgg /germline

A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data

annotation ngs germline cram ngs-pipeline genotyping germline-variant-calling short-reads

UpdatedMar 7, 2025
Nextflow

zhanghao-njmu /NGSmodule

A flexible, automation and pragmatic workflow tool to process the NGS data.

workflow rna-seq ngs wgs ngs-analysis ngs-pipeline

UpdatedDec 13, 2023
R

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