ngs-pipeline

There are 115 repositories under ngs-pipeline topic.

  • flowhub-team/awesome-omics

    A collection of awesome things regarding all omics.

    55135066

  • patidarr/ngs_pipeline

    Exome/Capture/RNASeq Pipeline Implementation using snakemake

    Language:Python456018
  • 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

    Language:R353217

  • ncbi/pm4ngs

    Project Manager for NGS data analysis

    Language:Python2718010

  • ncbi/cwl-ngs-workflows-cbb

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

    Language:Common Workflow Language2211510

  • viromelab/tracespipe

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

    Language:Shell22237

  • caulilin/QTG_Seq

    Language:R213010

  • epigen/open_pipelines

    Pipelines for NGS data preprocessing by the Bock lab and friends

    Language:Python20131511

  • 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

    Language:Nextflow195502

  • jnarayan81/setu

    SARS-CoV-2 Genome Assembler

    Language:Shell12102

  • angelovangel/nxf-fastqc

    A simple fastp-MultiQC nextflow pipeline

    Language:Nextflow11296

  • hivdb/codfreq

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

    Language:Python11652

  • NCBI-Hackathons/FlowBio

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

    Language:Shell111516

  • Hughes-Genome-Group/NGseqBasic

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

    Language:Shell10302

  • rusalkaguy/snakemake-slurm-tutorial

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

    Language:Python10201

  • bpucker/yam

    scripts associated with yam genome assembly

    Language:Python820

  • dmnfarrell/snipgenie

    command line and desktop tool for microbial variant calling

    Language:Jupyter Notebook8450

  • nf-core/denovohybrid

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

    Language:Nextflow8235

  • zhanghao-njmu/NGSmodule

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

    Language:R8203

  • JKlesmith/PACT

    Protein Analysis and Classifier Toolkit

    Language:Python7200
  • Lescroart2023

    jlescroart/Lescroart2023

    Archived code for analyses in "Extensive phylogenomic discordance and the complex evolutionary history of the Neotropical cat genus Leopardus" (Lescroart et al. 2023, MBE)

    Language:Python7200

  • nf-cmgg/germline

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

    Language:Nextflow73891

  • chopdgd/bfx-tools-wdl

    WDL tasks for commonly used BFX tools

    Language:WDL62625

  • csbbcompbio/CSBB-v3.0

    CSBB - Computational Suite For Bioinformaticians and Biologists

    Language:Perl6527

  • rcs333/CLOMP

    :horse: CLinically Okay Metagenomic Pipeline :horse:

    Language:Python6403

  • Sentieon/sentieon-google-genomics

    Run Sentieon pipelines on Google Cloud Platform

    Language:Shell6427

  • solida-core/solida

    SOLIDA is command-line solution that facilitate the reproducibility and portability of NGS pipelines. It can easily organize the deployment, the data management and the execution of a Snakemake based workflow.

    Language:Python6331

  • angelovangel/nextflow-fastp-shiny

    a shiny frontend for the nextflow-fastp pipeline

    Language:R5222

  • Barski-lab/biowardrobe

    BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data

    Language:JavaScript54111

  • hevmarriott/DNAscanv2

    DNAscan2 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

    Language:HTML5313

  • hyunhwan-jeong/CB2-Experiments

    CB2-Experiments is the repository of scripts and data of experiments were performed to benchmark the performance of CB2.

    Language:HTML5121

  • shanghungshih/ngs-main-wes

    This is dockerize "somatic paired-WES(Normal-Tumor) pipeline" which is refer to GATK best practice.

    Language:Python5100

  • V-Z/sondovac

    Sondovač is a script to create orthologous low-copy nuclear probes from transcriptome and genome skim data for target enrichment. For latest version check "releases".

    Language:TeX5463
  • ExpoSeq

    DigBioLab/ExpoSeq

    ExpoSeq is a pipeline to process and analyze in various visualizations ngs data from phage display campaigns

    Language:HTML4111

  • mehdimerbah/WES

    Whole Exome Sequencing end-to-end pipeline. Starting from whole exome fastq files: Data QC, Adapter Trimming, Reference Genome Alignment, SAM/BAM Validation, Data Recalibration and Variant Calling.

    Language:HTML4200

  • niekwit/pycrispr

    Pip package for CRISPR-Cas9 screen analysis

    Language:Python4100