GitHub topics: ngs-pipeline

Repositories

Replicon-genetics/rg_exploder_shared

Python code for generating synthetic sequence data: DNASEQ and RNASEQ reads for use as standards in genomics data analysis pipelines

Language: Python - Size: 209 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 0 - Forks: 0

jdieramon/master_biotec_NGS

Análisis genómicos y transcriptómicos con plataforma NGS

Language: HTML - Size: 6.68 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 0 - Forks: 0

CCBR/ASPEN

CCBR pipeline for preliminary QC, peak calling, differential chromatin accessibility analysis with ATACseq datasets 🌲

Language: Shell - Size: 620 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 0 - Forks: 0

TJ-lab-ustc/hDNApipe

Language: Shell - Size: 10.5 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 0 - Forks: 0

Sentieon/sentieon-google-genomics

Run Sentieon pipelines on Google Cloud Platform

Language: Shell - Size: 127 KB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 6 - Forks: 7

CCBR/CHARLIE

Circrnas in Host And viRuses anaLysis pIpEline for Detection Annotation Quantification of circRNAs

Language: Python - Size: 278 MB - Last synced at: 9 days ago - Pushed at: 11 days ago - Stars: 2 - Forks: 2

niekwit/rna-seq-star-tetranscripts

Snakemake workflow for transposable element RNA-Seq using TEtranscripts

Language: R - Size: 95.3 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 3 - Forks: 0

epigen/open_pipelines

Pipelines for NGS data preprocessing by the Bock lab and friends

Language: Python - Size: 549 KB - Last synced at: 7 days ago - Pushed at: over 2 years ago - Stars: 21 - Forks: 11

j-y26/Epigenomic-Pipelines

Standardized pipelines for processing epigenomic NGS data

Language: HTML - Size: 874 KB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 1 - Forks: 0

maurya-anand/nf-varcall

A Nextflow pipeline for variant calling and annotation using PacBio Hi-Fi sequencing reads.

Language: Nextflow - Size: 64.5 KB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 0 - Forks: 0

nf-cmgg/smallvariants

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

Language: Nextflow - Size: 10.4 MB - Last synced at: 9 days ago - Pushed at: 14 days ago - Stars: 8 - Forks: 1

biocoderdev/weap

WEAP: An automatic and accelerated pipeline for analysing multi-sample whole exome sequencing data

Language: Shell - Size: 2.64 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

dmnfarrell/snipgenie

command line and desktop tool for microbial variant calling

Language: Jupyter Notebook - Size: 133 MB - Last synced at: 7 days ago - Pushed at: about 2 months ago - Stars: 8 - Forks: 0

This pipeline processes high-throughput sequencing data (PE/SE) through QC,trim/filter,alignment,counting etc via sequential stages, with individual samples run in parallel via submission to a Slurm queue.

Language: Shell - Size: 154 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 1 - Forks: 0

plantinformatics/shortbread2

Shortbread2 is a bioinformatics pipeline for identifying single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) from High-Throughput Next Generation Sequencing (NGS) data.

Language: Perl - Size: 819 MB - Last synced at: about 2 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

MultipathogenGenomics/castanet

Application for analysis of targeted metagenomics sequencing data. Intended for use with multiplexed Illumina short-read data generated after enrichment.

Language: Python - Size: 100 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 3 - Forks: 0

chopdgd/bfx-tools-wdl

WDL tasks for commonly used BFX tools

Language: WDL - Size: 348 KB - Last synced at: 28 days ago - Pushed at: 2 months ago - Stars: 5 - Forks: 5

maxsonBraunLab/atac_seq

process and analyze paired-end ATAC-Seq data

Language: R - Size: 554 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 3 - Forks: 1

LeoooJR/ReproHackathon

A reproducible RNA-Seq analysis pipeline for Staphylococcus aureus under antibiotic stress, utilizing Nextflow and Singularity. It involves genome mapping, read counting, and statistical analysis to identify differentially expressed genes (DEGs) and generates key visualizations.

Language: R - Size: 158 KB - Last synced at: about 1 month ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

solida-core/dima

Snakemake pipeline to map DNA datasets to a given reference genome using BWA MEM and Samtools.

Language: Python - Size: 245 MB - Last synced at: 21 days ago - Pushed at: 5 months ago - Stars: 1 - Forks: 2

pritampanda15/NGS-Workflows

Next-generation Sequencing workflows

Language: Jupyter Notebook - Size: 275 MB - Last synced at: 6 days ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

lucianhu/Masterarbeit

Leveraging WES short reads for PAN-EXOME creation and analysis.

Language: WDL - Size: 18.6 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

srikanth-srinvas/dragonflye-hybrid-genome-assembly

Nextflow-powered Dragonflye Pipeline for Assembling Genomes from Nanopore and Illumina Reads

Language: Nextflow - Size: 224 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

IRI-UW-Bioinformatics/flu-ngs

NGS pipeline for influenza virus libraries

Language: Python - Size: 135 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 2 - Forks: 0

haseebmanzur/HackBio-Cancer-Internship

Here is my participation to the 2024 edition of the HackBio Internship (AMR in cancer track).

Language: R - Size: 1.07 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

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: Nextflow - Size: 5.37 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 19 - Forks: 2

V-Z/hybseq-scripts

Set of scripts to process HybSeq target enrichment HTS data (on computing grids).

Language: Shell - Size: 2.33 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 4 - Forks: 3

DigBioLab/ExpoSeq

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

Language: HTML - Size: 221 MB - Last synced at: 6 days ago - Pushed at: 9 months ago - Stars: 4 - Forks: 2

geniusphil/2024_digiplus_talent

2024 DIGI+ Talent跨域數位人才加速躍升計畫

Language: Shell - Size: 50 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 1 - Forks: 0

groverkaushal/Varying_kmer_effect_in_denovo_assembly

This project aims to observe the effect of selecting different kmer length parameter in 2 different de novo genome assembly tools - AbySS and Velvet.

Language: Python - Size: 1.45 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

Mayne941/castanet Fork of tgolubch/castanet

This repository has been ported to an employer workspace and is no longer maintained. Please refer to: https://github.com/MultipathogenGenomics/castanet

Language: Python - Size: 99.8 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0

CVUA-RRW/FooDMe

A reproducible and scalable snakemake workflow for the analysis of DNA metabarcoding experiments, with a special focus on food and feed samples.

Language: Python - Size: 3.54 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 3 - Forks: 1

NCBI-Hackathons/FlowBio

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

Language: Shell - Size: 210 MB - Last synced at: 6 months ago - Pushed at: over 6 years ago - Stars: 11 - Forks: 6

niekwit/pycrispr

Pip package for CRISPR-Cas9 screen analysis

Language: Python - Size: 1.15 MB - Last synced at: 8 days ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 1

viromelab/tracespipe

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

Language: Shell - Size: 15 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 18 - Forks: 7

DanielRCA/NCR-mtDNA_ampliconbasedngs

A free and easy-to-use pipeline to analyse data from ancient NCR-mtDNA sequences obtained by amplicon-based NGS methods

Language: Shell - Size: 21.6 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

lucianhu/Bash-script-DNA-Sequence

Linux command-line to analyse next-generation sequencing (NGS) data

Size: 103 KB - Last synced at: 11 months ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

renatosantos98/GLIMPSE-low-coverage-WGS-imputation

Supporting data for "Low-coverage whole genome sequencing for a highly selective cohort of severe COVID-19 patients"

Language: Python - Size: 28.7 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 2 - Forks: 0

ShuXingYu94/NGS_Process_Sample

Language: Shell - Size: 121 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 2 - Forks: 0

esohkevin/esohkevin.github.io

esohinformatics

Size: 25.1 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

folkehelseinstituttet/DiscoveryDocker Fork of garcia-nacho/DiscoveryDocker

Docker-based implementation of the Discover1.1 pipeline for bacterial characterization.

Language: Python - Size: 77.7 MB - Last synced at: 12 months ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

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: Python - Size: 126 KB - Last synced at: 12 months ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 1

RhettRautsaw/PhyProbe

PhyProbe is a bioinformatic pipeline designed to extract phylogenetic loci from Next-Generation Sequencing datasets including RNAseq, WGS, and Sequence/Target Capture methodologies (e.g., AHE, UCEs).

Language: Python - Size: 890 KB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 0

gozdekb/gozdekb

Basic packages for amplicon-based sequencing analysis.

Size: 8.79 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

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 Language - Size: 629 KB - Last synced at: 12 months ago - Pushed at: almost 2 years ago - Stars: 24 - Forks: 10

hivdb/codfreq

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

Language: Python - Size: 1.48 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 11 - Forks: 1

maurya-anand/make-pipeline

Variant calling pipeline for Pacbio Hifi reads

Language: Makefile - Size: 18.6 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

anand-imcm/pb-variant-call

Variant Calling and Annotation using PacBio Hi-Fi Reads

Language: WDL - Size: 59.6 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

nf-core/denovohybrid Fork of caspargross/nf-core-denovohybrid 📦

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

Language: Nextflow - Size: 2.55 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 8 - Forks: 3

flowhub-team/awesome-omics

A collection of awesome things regarding all omics.

Size: 123 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 535 - Forks: 61

NeuroSyd/ngs-variant-analysis

Novel mutations are identified in leukemia through variant analysis.

Size: 1.25 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

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: Python - Size: 623 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 0

mansikath/whole-genome-sequencing-pipeline

A comprehensive workflow for de novo assembly of whole-genome shotgun sequencing data using Velvet, followed by BLAST searches to analyze assembled contigs.

Language: HTML - Size: 1.96 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

Vzzarr/NGS-SparkGATK

An Efficient Design of a Next Generation Sequencing pipeline with Apache Spark

Language: PostScript - Size: 28.1 MB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 3 - Forks: 1

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: TeX - Size: 14.4 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 5 - Forks: 2

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: R - Size: 2.85 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 29 - Forks: 13

Hughes-Genome-Group/NGseqBasic

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

Language: Shell - Size: 408 KB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 10 - Forks: 2

shanghungshih/ngs-main-wes

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

Language: Python - Size: 313 KB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 5 - Forks: 0

tdayris-perso/ngs-cleaning 📦

Trimming and QC on NGS data

Language: Python - Size: 1.32 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 5

csbbcompbio/CSBB-v3.0

CSBB - Computational Suite For Bioinformaticians and Biologists

Language: Perl - Size: 4.7 MB - Last synced at: over 1 year ago - Pushed at: almost 7 years ago - Stars: 6 - Forks: 7

ncbi/pm4ngs

Project Manager for NGS data analysis

Language: Python - Size: 14 MB - Last synced at: 12 months ago - Pushed at: over 2 years ago - Stars: 25 - Forks: 10

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: HTML - Size: 4.2 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 3 - Forks: 0

tbersez/Allmine

AllMine, a flexible pipeline for Allele Mining. Develloped at INRA's GAFL unit :

Language: Python - Size: 5.74 MB - Last synced at: over 1 year ago - Pushed at: almost 6 years ago - Stars: 4 - Forks: 0

FSUgenomics/SRSFN

SRSF framework for nucleosome positioning analysis

Language: PostScript - Size: 329 KB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0

FSUgenomics/SRSFseq

SRSF shape analysis framework for sequencing data

Language: R - Size: 3.94 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 2

AbdelrahmanYahia/GUAP_toolkit

Genomics unit analysis pipelines toolkit: a collection of NGS workflows writtin in python3 and snakemake

Language: Python - Size: 1.83 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

patidarr/ngs_pipeline

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Language: Python - Size: 46.6 MB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 43 - Forks: 19

maingoc303/Graph_Genome

Language: HTML - Size: 14.8 MB - Last synced at: over 1 year ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

TC-Hewitt/MuTrigo

pipeline for mutant gene candidate discovery

Language: Python - Size: 81.1 KB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 0

zhanghao-njmu/NGSmodule

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

Language: R - Size: 1.98 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 2

svsuresh/ngs_scripts

This repository contains bash shell scripts

Language: R - Size: 9.77 KB - Last synced at: over 1 year ago - Pushed at: almost 7 years ago - Stars: 1 - Forks: 0

nicholascwho/TTE

Code used to analyze and produce figures during tenure in the Translational Tumor Engineering Lab

Language: R - Size: 53.7 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

AbdelrahmanYahia/wes_gatk

Whole exome sequencing snakemake workflow based on GATK best practice

Language: Jupyter Notebook - Size: 23.1 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1

lokapal/K562.hemin

Bioinformatic scripts for the manuscript concerning interchromosomal interaction and gene expression patterns of K562 cells treated by hemin

Language: R - Size: 5.62 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

rmoffitt/GeneSetMatch

A tool for deep statistical analyses and informative visualizations of complex -omic data

Language: HTML - Size: 189 MB - Last synced at: 13 days ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

niekwit/pyseqtools

Tools for NGS data analysis

Language: Python - Size: 658 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

Pg-Pi3Gey/ms-chikv-deg

main Repository for my Master's Thesis work

Language: R - Size: 10.7 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

caulilin/QTG_Seq

Language: R - Size: 8.64 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 20 - Forks: 10

mdraminski/CytoMeth

CytoMeth tool compiles a set of open source software named in the Roche pipeline guidelines to perform SeqCap Epi data analysis.

Language: R - Size: 45.5 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 1

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: HTML - Size: 78.5 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 1