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Search results for pipeline nextflow

189 search results found

Docker Benchmarks ⭐ 17

A benchmarks of genomic pipelines running in Docker containers

Pipelines for the production of Treeval data

Bactpipe ⭐ 17

BACTpipe: An assembly and annotation pipeline for bacterial genomics

Piper Nf ⭐ 17

RNA mapping pipeline

A pipeline to investigate horizontal gene transfer from NGS data

Crg Course Nov16 ⭐ 17

Nextflow + Docker tutorial material

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.

Genomenote ⭐ 16

This Nextflow DSL2 pipeline takes aligned HiC reads, creates contact maps and a table of statistics.

Pipeline for Universal Mapping of ATAC-seq

The Microbial Co-occurrence Network Explorer

Sc2 Illumina Pipeline ⭐ 14

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

CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.

Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.

Nf Anvio Pangenome ⭐ 14

Analyze a set of genomes with the anvi'o pangenome pipeline

An automated ChIP-seq pipeline using Nextfow

UNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies

AMR/VF LGT focused bacterial genomics analysis workflow

Exllsm Circuit Reconstruction ⭐ 12

Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery

Genomeassembler ⭐ 12

A tooL for Prokaryotic Phylogeny And Clustering Analysis

Metaboigniter ⭐ 11

Pre-processing of mass spectrometry-based metabolomics data with quantification and identification based on MS1 and MS2 data.

Image Mass Cytometry analysis pipeline

Genomeannotator ⭐ 11

Pipeline for the identification of (coding) gene structures in draft genomes.

Chipimputation ⭐ 11

Genotype Imputation Pipeline for H3Africa

Plasmident ⭐ 10

Atacflow ⭐ 10

An ATAC-seq pipeline wrapped in NextFlow that can be run by Jupyter

A pipeline for comprehensive genomic analyses of Mycobacterium tuberculosis with a focus on clinical decision making as well as research

Assembly and intrahost / low-frequency variant calling for viral samples

Polishclr ⭐ 10

A nextflow pipeline for polishing CLR assemblies

Standardized and Automated MetaBarcoding Analyses workflow (Mirror)

Nxf Kraken2 ⭐ 10

A simple nextflow pipeline for running kraken2 and bracken in a docker container

Bamtofastq ⭐ 10

Converts bam or cram files to fastq format and does quality control.

MONSDA, Modular Organizer of Nextflow and Snakemake driven hts Data Analysis

Tostadas ⭐ 10

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

Rmghc 2018 ⭐ 10

Nextflow Workshop at Rocky Mountain Genomics HackCon 2018

Please consider using/contributing to https://github.com/nf-core/sarek

Cellatac ⭐ 10

Sanger Cellular Genetics single-cell ATAC-seq pipeline.

Functional annotation pipeline for proteins from non-model organisms implemented in Nextflow

Blobtoolkit ⭐ 9

Nextflow pipeline for BlobToolKit for Sanger ToL production suite

Viralintegration ⭐ 9

Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.

Gwas Tools ⭐ 9

🧬 Containerized pipelines for GWAS

Nf Whisper ⭐ 9

Proof-of-concept Nextflow pipeline to interact with OpenAI Whisper

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

Nascent Flow ⭐ 8

Nascent Transcription Processing Pipeline

Fastquorum ⭐ 8

Wgs Structvar ⭐ 8

Whole Genome Sequenceing Structural Variation Pipelines

Nextflow_pipelines ⭐ 8

The set of NGS processing pipelines used at Babraham

Fast RNAseq pipeline

Readsimulator ⭐ 8

A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.

Goodbioinfo2018 ⭐ 8

Course on good practice in bioinformatics

k-mer similarity analysis pipeline

Gatk4 Germline Snps Indels ⭐ 8

Workflow for germline short variant discovery using GATK4

Ngi Chipseq ⭐ 7

Nextflow ChIP-seq data analysis pipeline, National Genomics Infrastructure, Science for Life Laboratory in Stockholm

Dualrnaseq ⭐ 7

Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.

Multigranular Analysis of Regulatory Variants on the Epigenomic Landscape

Rnaseq Flow ⭐ 7

Nextflow pipeline for processing RNA-seq data

Scrnaseq_pipelines ⭐ 7

Staphopia Ap ⭐ 7

Nf Phdcourse19 ⭐ 7

Nextflow training material for CRG PhD course 2019

MNase-seq analysis pipeline using BWA and DANPOS2.

Ngs580 Nf ⭐ 7

Target exome sequencing analysis for NYU NGS580 gene panel

Kallisto Sra ⭐ 7

Nextflow bioinformatics pipeline for large-scale analysis of Multiple Myeloma genomes

Multiplesequencealign ⭐ 7

A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.

A nextflow pipeline for performing bacterial RNA-Seq data analysis.

This pipeline will run QC measures of both genotype and phenotype data and will normalise quantified phenotypes

Gps Pipeline ⭐ 6

Nextflow Pipeline for processing Streptococcus pneumoniae sequencing raw reads (FASTQ files) by the GPS Project (Global Pneumococcal Sequencing Project)

Phageannotator ⭐ 6

Pipeline for identifying, annotation, and quantifying phage sequences in (meta)-genomic sequences.

Mikrokondo ⭐ 6

A simple pipeline for bacterial assembly and quality control

Ramdaq Prototype ⭐ 6

Quality control pipeline for RamDA-seq experiments.

Configbuilder Nf ⭐ 6

Nextflow config builder scripts for supported HPC infrastructures.

Cleansumstats ⭐ 6

Convert GWAS sumstat files into a common format with a common reference for positions, rsids and effect alleles.

Nederlab Pipeline ⭐ 6

Linguistic enrichment pipeline for historical dutch, as used in the Nederlab project

Kube Runner ⭐ 6

A tool for running bioinformatics workflows on a Kubernetes cluster

Nanostring ⭐ 6

An analysis pipeline for Nanostring nCounter expression data.

Genome Annotation ⭐ 6

A nextflow pipeline with automatic software provisioning to generate hints and subsequent genome model predictions with AUGUSTUS

Readmapping ⭐ 6

Nextflow DSL2 pipeline to align short and long reads to genome assembly. This workflow is part of the Tree of Life production suite.

Speaqeasy ⭐ 6

SPEAQeasy: portable LIBD RNA-seq pipeline using Nextflow. Check http://research.libd.org/SPEAQeasy-example/ for an example on how to use this pipeline and analyze the resulting output files.

Tofu Maapo ⭐ 6

Nextflow pipeline for the analysis of metagenomic short reads.

From metagenomes to epitopes and beyond

Gccbosc18 Training ⭐ 6

Documentation for Nextflow training at GCC/BOSC 2018

Nascent Transcription Processing Pipeline

Nf Repeatmasking ⭐ 5

Nextflow workflow for automatic repeat detection, classification and masking

CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.

Nextflow Course 2018 ⭐ 5

IARC nextflow course for pipeline users

Rnaseq_bybabs ⭐ 5

Nextflow RNA-Seq Analysis Pipeline

Metaboigniter ⭐ 5

Pre-processing of mass spectrometry-based metabolomics data with quantification and identification based on MS1 and MS2 data

Nf Encyclopedia ⭐ 5

A NextFlow pipeline for chromatogram library DIA proteomics workflows

Integrative Pipeline for Splicing Analyses (IPSA) in Nextflow

Epitypification pipeline for clinical NGS data. Written in NextFlow, Python & Bash.

A pipeline for metabarcoding fungi and other eukaryotes with full-length ITS sequenced with PacBio

Scenic Nf ⭐ 5

DEPRECATED | pySCENIC pipeline implemented in Nextflow using containers

Genomeassembly ⭐ 5

Implementation of ToL genome assembly workflows

Nxf Fastqc ⭐ 5

A simple fastp-MultiQC nextflow pipeline

Ribomethseq Nf ⭐ 5

Nextflow pipeline dedicated to RiboMethSeq data processing

Wf Human Mito ⭐ 5

Workflow for human mitochondria analysis

A simple nextflow pipeline for Illumina run metrics (InterOp) and generation of fastq files (bcl2fastq)

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