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Search results for nextflow
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362 search results found
Deepvariant
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26
Deep Variant as a Nextflow pipeline
Proteinfold
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26
Protein 3D structure prediction pipeline
Gemmaker
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26
A workflow for construction of Gene Expression count Matrices (GEMs). Useful for Differential Gene Expression (DGE) analysis and Gene Co-Expression Network (GCN) construction
Nf Lo
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26
A Nextflow workflow to generate lift over files for any pair of genomes
Geneshot
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25
Pipeliner
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25
A flexible Nextflow-based framework for the definition of sequencing data processing pipelines
Rnatoy
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24
A proof of concept RNA-Seq pipeline with Nextflow
Rnavar
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23
gatk4 RNA variant calling pipeline
Wave
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23
On-demand containers provisioning service
Ngs Preprocess
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23
A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies
Compare_genomes
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23
A comparative genomics workflow using Nextflow, conda, Julia and R
Bionextflow
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22
A collection of modules and sub-workflows for Nextflow
Nextflowmodules
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22
UMCU Genetics Nextflow modules
Macse_v2_pipelines
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21
This repository provides source code for several pipelines dedicated to the alignment of nucleotide coding sequences that are based on MACSE. These pipelines are mostly bash scripts encapsulated within singularity containers and sometimes combined in nextflow workflows.
Naf_dataset
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21
Form images from U.S. National Archives annotated with text bounding boxes, classes, relationships, and transcription.
Clean
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21
A nextflow pipeline for decontamination of short reads, long reads and contigs
Nextflow Example
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20
A simple DSL2 workflow: tutorial
Spandx
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20
SPANDx - Comparative genomics for next-generation haploid sequence data
Rnaseq Nf
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20
RNAseq analysis pipeline
Kallisto Nf
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20
A nextflow implementation of Kallisto & Sleuth RNA-Seq Tools
Nanoflow
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20
🔬 De novo assembly of nanopore reads using nextflow
Variant_catalogue_pipeline
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20
Variant catalogue pipeline
Mop2
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20
Master of Pores 2
Mycosnp Nf
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20
CDCgov/mycosnp-nf
Porefile
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19
A Nextflow full-length 16S profiling pipeline for ONT reads
Companion
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19
Pipeline for automatic eukaryotic parasite annotation
Wf Basecalling
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19
Spew
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19
Automatic Packaging and Distribution of Bioinformatics Pipelines
Maliampi
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19
Maximum Likelihood Amplicon Pipeline
Sublime Nextflow
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19
Nextflow workflow syntax highlighting and snippets for Sublime Text 4
Tada
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19
TADA - Targeted Amplicon Diversity Analysis - a DADA2-focused Nextflow workflow for any targeted amplicon region
Wf Pore C
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18
Gatk4_best_practice
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18
GATK4 Best Practice Nextflow Pipeline
Metagenomics
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18
A Nextflow workflow for QC, evaluation, and profiling of metagenomic samples using short- and long-read technologies
Rnasplice
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18
rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis
Lncpipe
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18
UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets
Alignment Nf
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18
Whole Exome/Whole Genome Sequencing alignment pipeline
Cookiecutter
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18
DEPRECIATED! Please use nf-core/tools instead
Circdna
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18
Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.
Crisprseq
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17
A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).
Crg Course Nov16
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17
Nextflow + Docker tutorial material
Nf Gwas Pipeline
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17
A Nextflow Genome-Wide Association Study (GWAS) Pipeline
Quantms
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17
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
Docker Benchmarks
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17
A benchmarks of genomic pipelines running in Docker containers
Workflows Nextflow
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17
Workflow management with Nextflow and nf-core
Piper Nf
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17
RNA mapping pipeline
Hgtseq
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17
A pipeline to investigate horizontal gene transfer from NGS data
Treeval
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17
Pipelines for the production of Treeval data
Bactpipe
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17
BACTpipe: An assembly and annotation pipeline for bacterial genomics
Idplot
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17
compare sequences to a shared root reference sequence.
Nextflow Mode
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16
Emacs major mode for Nextflow
Genomenote
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16
This Nextflow DSL2 pipeline takes aligned HiC reads, creates contact maps and a table of statistics.
Neoflow
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16
NeoFlow: a proteogenomics pipeline for neoantigen discovery
Pocp
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16
Calculation of the Percentage of Conserved Proteins following Qin, Xie et al. 2014
Pumatac
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16
Pipeline for Universal Mapping of ATAC-seq
Amrplusplus
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16
Wave Showcase
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16
Examples showing how to configure Nextflow to run with Wave containers provisioning service
Vscode Language Nextflow
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15
Nextflow language support for Visual Studio Editor
Nf Flu
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15
Influenza genome analysis Nextflow workflow
Covigator Ngs Pipeline
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15
A Nextflow pipeline for NGS variant calling on SARS-CoV-2. From FASTQ files to normalized and annotated VCF files from GATK, BCFtools, LoFreq and iVar.
Dockstore Ui2
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15
Website user interface for Dockstore in Angular2
Micone
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15
The Microbial Co-occurrence Network Explorer
Clipseq
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14
CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.
Dryad
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14
Dryad is a pipeline to construct reference free core-genome or SNP phylogenetic trees for examining prokaryote relatedness in outbreaks.
Hadge
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14
Comprehensive pipeline for donor demultiplexing in single cell
Isoseq
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14
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
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14
Analyze a set of genomes with the anvi'o pangenome pipeline
Sc2 Illumina Pipeline
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14
Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub
Splicing Pipelines Nf
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14
Repository for the Anczukow-Lab splicing pipeline
Viroprofiler
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14
A containerized bioinformatics pipeline for viral metagenomic data analysis
Chip Nf
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13
An automated ChIP-seq pipeline using Nextfow
Nf Hack18
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13
Nextflow workshop 2018 -- Training pages -> https://nextflow-io.github.io/nf-hack18/
Grandeur
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13
UPHL's Reference Free Pipeline
Transpi
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13
TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly
Webinarpipeline
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12
Please don't break!!
Hic Scaffolding Nf
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12
Nextflow pipeline for scaffolding genome assemblies with Hi-C reads
Gwas
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12
UNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies
Genomeassembler
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12
Geneidx
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12
Nextflow pipeline for genome annotation of protein-coding genes
Hyperopt
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12
Nextflow pipeline for hyperparameter optimization of machine learning models
Bohra
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12
A pipeline for bioinformatics analysis of bacterial genomes
Arete
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12
AMR/VF LGT focused bacterial genomics analysis workflow
Exllsm Circuit Reconstruction
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12
Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery
Taxtriage
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11
TaxTriage is designed in concordance with CDC recommendations to provide clinical environments the necessary tools to generate classification reports (using Kraken2) in a metagenomics scope. It is bundled with Nextflow to provide a seamless installation and usage experience. It is currently being developed as an alpha version and is intended for a full release by October of 2022
Alppaca
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11
A tooL for Prokaryotic Phylogeny And Clustering Analysis
Viralclust
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11
Small pipeline to cluster viral genomes based on their k-mer content. WiP
Ramdaq
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11
Machine_learning_determinism_evaluation
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11
GPU deterministic machine learning with Nextflow
Lodestone
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11
Mycobacterial pipeline
Imcyto
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11
Image Mass Cytometry analysis pipeline
Metaboigniter
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11
Pre-processing of mass spectrometry-based metabolomics data with quantification and identification based on MS1 and MS2 data.
Cactus
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11
Chromatin ACcessibility and Transcriptomics Unifying Software
Chipimputation
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11
Genotype Imputation Pipeline for H3Africa
Scpca Nf
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11
scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data
Octapus
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11
Bacterial Operon Finder for Functional Organization
Genomeannotator
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11
Pipeline for the identification of (coding) gene structures in draft genomes.
Samba
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10
Standardized and Automated MetaBarcoding Analyses workflow (Mirror)
Magma
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10
A pipeline for comprehensive genomic analyses of Mycobacterium tuberculosis with a focus on clinical decision making as well as research
Bamtofastq
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10
Converts bam or cram files to fastq format and does quality control.
Monsda
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10
MONSDA, Modular Organizer of Nextflow and Snakemake driven hts Data Analysis
Related Searches
Pipeline Nextflow (284)
Nextflow Nf Core (75)
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Genome Nextflow (65)
Docker Nextflow (58)
Sequencing Nextflow (33)
Fastq Nextflow (31)
Python Nextflow (30)
101-200 of 362 search results
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