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Search results for pipeline sequencing

114 search results found

Galaxy ⭐ 1,211

Data intensive science for everyone.

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Copy number variant detection from targeted DNA sequencing

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Snapatac ⭐ 227

Analysis Pipeline for Single Cell ATAC-seq

UGENE is free open-source cross-platform bioinformatics software

Sunbeam ⭐ 157

A robust, extensible metagenomics pipeline

Ampliseq ⭐ 141

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Sequana ⭐ 136

Sequana: a set of Snakemake NGS pipelines

Rnaseq Workflow ⭐ 133

A repository for setting up a RNAseq workflow

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.

Methylseq ⭐ 121

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

Rnalysis ⭐ 114

RNA sequencing analysis software

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

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

A handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.

Rna Seq Pipeline ⭐ 88

Hybpiper ⭐ 83

Recovering genes from targeted sequence capture data

Making whole bacterial genome sequencing data analysis easy

Nanopype ⭐ 78

Snakemake pipelines for nanopore sequencing data archiving and processing

Master_of_pores ⭐ 77

Nextflow pipeline for analysis of direct RNA Nanopore reads

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

Neoantigen Vaccine Pipeline ⭐ 72

Bioinformatics pipeline for selecting patient-specific cancer neoantigen vaccines

Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)

Smrnaseq ⭐ 63

A small-RNA sequencing analysis pipeline

Methpipe ⭐ 63

A pipeline for analyzing DNA methylation data from bisulfite sequencing.

Pyflow Chipseq ⭐ 55

a snakemake pipeline to process ChIP-seq files from GEO or in-house

Pipelines for the analysis of 10x single-cell RNA-sequencing data

Pipeline Standardization ⭐ 47

Simple bacterial assembly and annotation pipeline

a bash pipeline for RAD sequencing

Ncov Tools ⭐ 44

Small collection of tools for performing quality control on coronavirus sequencing data and genomes

A RepSeq processing swiss-knife

Hic_pipeline ⭐ 40

An easy-to-use Hi-C data processing software supporting distributed computation.

Needlestack ⭐ 39

Multi-sample somatic variant caller

Ngstools ⭐ 37

Next-Generation Sequencing(NGS) toolkits.

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.

Hlatyping ⭐ 34

Precision HLA typing from next-generation sequencing data

Covid 19 Signal ⭐ 32

Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.

Nano Snakemake ⭐ 31

A snakemake pipeline for SV analysis from nanopore genome sequencing

Amplicon_sequencing_pipeline ⭐ 30

Pipeline for computing OTU tables from 16S or ITS amplicon sequencing data.

Wochenende ⭐ 30

Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3

The open source version of the Melbourne Genomics Health Alliance Exome Sequencing Pipeline

RNASeq pipeline

Idseq Workflows ⭐ 27

Portable WDL workflows for IDseq production pipelines

Long Read Proteogenomics ⭐ 26

A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.

Pipeliner ⭐ 25

A flexible Nextflow-based framework for the definition of sequencing data processing pipelines

Ctdna Pipeline ⭐ 24

A simplified pipeline for ctDNA sequencing data analysis

Dna Me Pipeline ⭐ 24

DCC/DAC methylation pipeline source

A scalable cloning system

gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (WGBS).

A genomics pipeline build on top of the GATK Queue framework. Main repository: https://github.com/NationalGenomicsInfrastructure/ (make sure you fork from there)

Gnomad Sv Pipeline ⭐ 22

Code and custom scripts relevant to gnomAD-SV (Collins*, Brand*, et al., 2020)

Amrplusplus_v2 ⭐ 21

MEGARes and AmrPlusPlus - A comprehensive database of antimicrobial resistance genes and user-friendly pipeline for analysis of high-throughput sequencing data

Open-source bioinformatics pipeline for the preprocessing of raw sequencing data.

A pipeline to assess the quantification of transcripts.

Gatk4_best_practice ⭐ 18

GATK4 Best Practice Nextflow Pipeline

Hlatools ⭐ 17

A series of tools and pipelines for genotyping MHC / HLA genes and alleles using SMRT Sequencing

Pipeline for Universal Mapping of ATAC-seq

Methylstar ⭐ 16

A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.

Dnbelab_c_series_scrna Analysis Software ⭐ 16

An open source and flexible pipeline to analyze DNBelab C Series single-cell RNA datasets.

Clinicalgradednaseq ⭐ 15

Automated next generation DNA sequencing analysis pipeline suited for clinical tests, with >99.9% sensitivity to Sanger sequencing at read-depth>18

Roslin Variant ⭐ 15

Roslin is a reproducible and reusable workflow for Cancer Genomic Sequencing Analysis

Sc2 Illumina Pipeline ⭐ 14

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

Proseq2.0 ⭐ 14

Preprocesses and Aligns Run-On Sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing

Microbiome_notes ⭐ 13

A continually expanding collection of microbiome analysis tools

Cl Elprep ⭐ 12

elPrep: a high-performance tool for preparing sequencing alignment/map files in sequencing pipelines (Lisp version)

Dib Mmetsp ⭐ 12

Code to generate re-assemblies of the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP)

Sars Cov 2_multi Pcr_v1.0 ⭐ 12

SARS-CoV-2 analysis pipeline for multiplex-PCR MPS(Massive Parrallel Sequencing) data

Ngs Pipeline ⭐ 12

Pipeline for Somatic Variant Calling with WES and WGS data

Pipeline ⭐ 12

Node.js module for simplifying and sequencing a number of dependent functions and callbacks.

Zika Seq ⭐ 12

Pipelines to do MinION sequencing of Zika virus

seqqs is a C program/library for gathering quality statistics from sequencing data

hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data

Illumina analysis pipeline

Deepvariant On Spark ⭐ 11

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

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

NGS perl modules

INC-Seq: Accurate single molecule reads using nanopore sequencing

Exseqprocessing ⭐ 10

Python-based pipeline for analyzing Nanopore sequencing metabarcoding data

Damidseq_pipeline ⭐ 10

An automated pipeline for processing DamID sequencing datasets

Pipeline for Evaluating Prokaryotic References

Tostadas ⭐ 10

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

Npg_seq_pipeline ⭐ 9

Processing and analysis of data coming from Illumina sequencing machines

Sequencer Js ⭐ 9

Library of sequencing patterns

Sc_gestalt ⭐ 9

GESTALT processing pipeline for barcodes captured with single-cell RNA sequencing

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

A python-based isomiR quantification and analysis pipeline

Wgs_sample_preparation ⭐ 9

Trim, Align to genome, Deduplicate, Realign WGS sequencing samples

Pdx_exomeseq ⭐ 9

Pipeline analysis for whole exome sequencing of pancreatic cancer PDX models

16s Dada2 ⭐ 8

Snakemake pipeline for amplicon sequencing using dada2

Shotgun Metagenomics Pipeline ⭐ 8

A pipeline for primary analysis of shotgun metagenomic sequencing data

A comprehensive quality-control and quantification RNA-seq pipeline

Cemba_data ⭐ 8

Mapping pipeline for snmC-seq based technologies.

Dnaseq_pipeline ⭐ 8

Pipeline in place at the UGI for DNA level analysis

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