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Search results for pipeline bioinformatics
bioinformatics
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pipeline
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164 search results found
Nextflow
⭐
2,447
A DSL for data-driven computational pipelines
Galaxy
⭐
1,211
Data intensive science for everyone.
Scipipe
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1,010
Robust, flexible and resource-efficient pipelines using Go and the commandline
Rush
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782
A cross-platform command-line tool for executing jobs in parallel
Juicer
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313
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Sarek
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299
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Bedops
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244
🔬 BEDOPS: high-performance genomic feature operations
Bpipe
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220
Bpipe - a tool for running and managing bioinformatics pipelines
Tools
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205
Python package with helper tools for the nf-core community.
Ugene
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190
UGENE is free open-source cross-platform bioinformatics software
Mag
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164
Assembly and binning of metagenomes
Gatk Sv
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148
A structural variation pipeline for short-read sequencing
Rnaseq Workflow
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133
A repository for setting up a RNAseq workflow
Seq2science
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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.
Sarek
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126
Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
Redundans
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121
Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
Rnalysis
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114
RNA sequencing analysis software
Eager
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112
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
Cloops
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99
Accurate and flexible loops calling tool for 3D genomic data.
Biojupies
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94
Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.
Dolphinnext
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92
A graphical user interface for distributed data processing of high throughput genomics
Fermikit
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91
De novo assembly based variant calling pipeline for Illumina short reads
Ilus
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89
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.
Arcs
⭐
86
🌈Scaffold genome sequence assemblies using linked or long read sequencing data
Flowr
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83
Robust and efficient workflows using a simple language agnostic approach
Plant Seg
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81
A tool for cell instance aware segmentation in densely packed 3D volumetric images
Tasks
⭐
78
A collection of reusable WDL tasks. Category:Other
Taxprofiler
⭐
78
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Callings Nf
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76
GATK RNA-Seq Variant Calling in Nextflow
Configs
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73
Config files used to define parameters specific to compute environments at different Institutions
Cosmos2
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72
Python Scientific Pipeline Management System
Tibanna
⭐
68
Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.
Scatac Pro
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64
A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
Aviary
⭐
62
A hybrid assembly and MAG recovery pipeline (and more!)
Tomicsvis
⭐
50
Transcriptomics Visualization R package.
Ngi Rnaseq
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49
Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
Funcscan
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49
(Meta-)genome screening for functional and natural product gene sequences
Pipeline Builder
⭐
48
Pipeline Builder is a JavaScript library for visualizing and constructing bioinformatics workflows, using Workflow Description Language (WDL)
Asap
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46
A scalable bacterial genome assembly, annotation and analysis pipeline
Microbiomebestpracticereview
⭐
45
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
Bio Pipeline
⭐
45
My collection of light bioinformatics analysis pipelines for specific tasks
Bistro
⭐
44
A library to build and execute typed scientific workflows
Mtoolbox
⭐
44
A bioinformatics pipeline to analyze mtDNA from NGS data
Metasra Pipeline
⭐
42
MetaSRA: normalized sample-specific metadata for the Sequence Read Archive
Pypiper
⭐
42
Python toolkit for building restartable pipelines
Migec
⭐
40
A RepSeq processing swiss-knife
Hic_pipeline
⭐
40
An easy-to-use Hi-C data processing software supporting distributed computation.
Pipelines.jl
⭐
39
A lightweight and powerful Julia package for computational pipelines and workflows.
Janis
⭐
39
[Alpha] Janis: an open source tool to machine generate type-safe CWL and WDL workflows
Dnapipete
⭐
38
dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X).
Rubra
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37
Infrastructure code to support DNA pipeline
Dee2
⭐
37
Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data
Mpox
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37
Nextstrain build for mpox virus
Qtlmap
⭐
36
Portable eQTL analysis and statistical fine mapping workflow used by the eQTL Catalogue
Iarc Nf
⭐
35
List of IARC bioinformatics nextflow pipelines
Bionode Watermill
⭐
34
💧Bionode-Watermill: A (Not Yet Streaming) Workflow Engine
Spatialtranscriptomics
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34
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
Circrna
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32
circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
Covid 19 Signal
⭐
32
Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
Reademption
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31
A pipeline for the computational evaluation of RNA-Seq data
Wochenende
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30
Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3
Pgcgap
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29
The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline
Epitopeprediction
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28
A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
Hichipper
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28
A preprocessing and QC pipeline for HiChIP data
Judi
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27
This repository contains the source code of JUDI, a workflow management system for developing complex bioinformatics software with many parameter settings. Bioinformatics pipeline: Just Do It!
Busco_phylogenomics
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26
BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins
Biokepi
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26
Bioinformatics Ketrew Pipelines
Perl For Bioinformatics
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26
An attempt to help anyone interested in using Perl for Bioinformatics
Genipe
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26
Genome-wide imputation pipeline
Snapr
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25
SNAPR: a bioinformatics pipeline for efficient and accurate RNA-seq alignment and analysis
Pipeliner
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25
A flexible Nextflow-based framework for the definition of sequencing data processing pipelines
Atacseq_pipeline
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25
Ultimate ATAC-seq Data Processing & Quantification Workflow. A Snakemake implementation of the BSF's ATAC-seq Data Processing Pipeline extended by downstream quantification and annotation steps using bash and Python.
Pyrpipe
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25
Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
Asap
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24
ASAP : Automated Single-cell Analysis Pipeline
Jamp
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24
JAMP - Just Another Metabarcoding Pipeline
Ctdna Pipeline
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24
A simplified pipeline for ctDNA sequencing data analysis
Phylociraptor
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23
rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference
Nanome
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23
NANOME pipeline (Nanopore long-read sequencing data consensus DNA methylation detection)
Ngs Preprocess
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23
A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies
Smbl
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22
SMBL - SnakeMake Bioinformatics Library. Automatic installation of bioinformatics software in your SnakeMake pipelines.
Bionextflow
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22
A collection of modules and sub-workflows for Nextflow
Sv Pipeline
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21
Pipeline for structural variation detection in cohorts
Rna Seq Snakemake
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20
Snakemake based pipeline for RNA-Seq analysis
Zika Pipeline
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19
The Zika bioinformatics pipeline
Kgwasflow
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19
kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
Pigx_rnaseq
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19
Pipeline for RNAseq
Companion
⭐
19
Pipeline for automatic eukaryotic parasite annotation
Mosaicatcher Pipeline
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19
Integrated workflow for SV calling from single-cell Strand-seq data
Piquant
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18
A pipeline to assess the quantification of transcripts.
Rnaseq Pipeline
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18
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
Cookiecutter
⭐
18
DEPRECIATED! Please use nf-core/tools instead
Gatk4_best_practice
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18
GATK4 Best Practice Nextflow Pipeline
Bactpipe
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17
BACTpipe: An assembly and annotation pipeline for bacterial genomics
Open_pipelines
⭐
17
Pipelines for NGS data preprocessing by the Bock lab and friends
Pipernaseq
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16
A comprehensive pipeline for RNAseq data analysis
Metasub_cap
⭐
16
A comprehensive pipeline for short read metagenomic data
Doepipeline
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16
A python package for optimizing processing pipelines using statistical design of experiments (DoE).
Pigx_sars Cov 2
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16
PiGx SARS-CoV-2 wastewater sequencing pipeline
Rmap
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15
Bacterial analysis Toolbox for profiling the Resistome of ESKAPE pathogens using WGS
Parser
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15
parseR: Pipeline for rna-seq analysis in R
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