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Search results for bioinformatics pipeline
bioinformatics-pipeline
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181 search results found
Scipipe
⭐
1,010
Robust, flexible and resource-efficient pipelines using Go and the commandline
Reflow
⭐
946
A language and runtime for distributed, incremental data processing in the cloud
Bacalhau
⭐
614
Compute over Data framework for public, transparent, and optionally verifiable computation
Pysradb
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269
Package for fetching metadata and downloading data from SRA/ENA/GEO
Snapatac
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227
Analysis Pipeline for Single Cell ATAC-seq
Roary
⭐
219
Rapid large-scale prokaryote pan genome analysis
Circlator
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193
A tool to circularize genome assemblies
Artemis
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191
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
Gcp For Bioinformatics
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178
GCP for Bioinformatics Researchers
Snp Sites
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173
Finds SNP sites from a multi-FASTA alignment file
Ngless
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141
NGLess: NGS with less work
Ariba
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135
Antimicrobial Resistance Identification By Assembly
Atac_dnase_pipelines
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135
ATAC-seq and DNase-seq processing pipeline
Gubbins
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133
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
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.
Toga
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120
TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.
V Pipe
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119
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
Methylpy
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116
WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
Rnalysis
⭐
114
RNA sequencing analysis software
Open Cravat
⭐
98
A modular annotation tool for genomic variants
Too Many Cells
⭐
95
Cluster single cells and analyze cell clade relationships with colorful visualizations.
Ilus
⭐
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.
Wholegenomesequencing
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86
Whole Genome Sequencing analysis, WGS analysis
Tasks
⭐
78
A collection of reusable WDL tasks. Category:Other
Czid Web
⭐
75
Infectious Disease Sequencing Platform
Zika Rnaseq Pipeline
⭐
73
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study
Neoantigen Vaccine Pipeline
⭐
72
Bioinformatics pipeline for selecting patient-specific cancer neoantigen vaccines
Altanalyze
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72
AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.
Ggcat
⭐
60
Compacted and colored de Bruijn graph construction and querying
Snakecharm
⭐
58
Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.
Chitin
⭐
56
chitin: an awful shell for awful bioinformaticians
Awesome Structural Bioinformatics
⭐
54
Structural Bioinformatics is awesome. Throw your textbook in the garbage, light the garbage can on fire, and blend the ashes into your cold brew almond milk latte and read this.
Eoulsan
⭐
50
A pipeline and a framework for NGS analysis (RNA-Seq and soon Chip-Seq)
R2g
⭐
49
A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
Mtoolbox
⭐
44
A bioinformatics pipeline to analyze mtDNA from NGS data
Finder
⭐
44
A fully automated gene annotator from RNA-Seq expression data
Phigaro
⭐
43
Phigaro is a scalable command-line tool for predicting phages and prophages
Metage2metabo
⭐
42
From annotated genomes to metabolic screening in large scale microbiotas
Pypiper
⭐
42
Python toolkit for building restartable pipelines
Bystro
⭐
40
Bystro genetic analysis (annotation, filtering, statistics)
Pipelines.jl
⭐
39
A lightweight and powerful Julia package for computational pipelines and workflows.
Assembly_improvement
⭐
39
Improve the quality of a denovo assembly by scaffolding and gap filling
Nphase
⭐
39
Ploidy agnostic phasing pipeline and algorithm
Iva
⭐
37
de novo virus assembler of Illumina paired reads
Oliver
⭐
36
An opinionated Cromwell orchestration manager.
Dnascan
⭐
36
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.
Grein
⭐
30
GREIN : GEO RNA-seq Experiments Interactive Navigator
Conda Env Builder
⭐
30
Build and maintain multiple custom conda environments all in one place.
Micropipe
⭐
30
A pipeline for high-quality bacterial genome construction using ONT sequencing
Lsf
⭐
29
Snakemake profile for running jobs on an LSF cluster
Skymap
⭐
28
High-throughput gene to knowledge mapping through massive integration of public sequencing data.
Bioqueue
⭐
28
A novel pipeline framework to accelerate bioinformatics analysis
Virtus
⭐
28
A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.
Judi
⭐
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!
Pisces
⭐
26
PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.
Omicselector
⭐
26
OmicSelector - Environment, docker-based application and R package for biomarker signiture selection (feature selection) & deep learning diagnostic tool development from high-throughput high-throughput omics experiments and other multidimensional datasets. Initially developed for miRNA-seq, RNA-seq and qPCR.
Biokepi
⭐
26
Bioinformatics Ketrew Pipelines
Speciesprimer
⭐
26
The SpeciesPrimer pipeline is intended to help researchers finding specific primer pairs for the detection and quantification of bacterial species in complex ecosystems.
Pyrpipe
⭐
25
Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
Snapr
⭐
25
SNAPR: a bioinformatics pipeline for efficient and accurate RNA-seq alignment and analysis
Asap
⭐
24
ASAP : Automated Single-cell Analysis Pipeline
Seqsender
⭐
24
Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
Snatac
⭐
23
<<------ Use SnapATAC!!
Gembs
⭐
23
gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (WGBS).
Socru
⭐
23
Order and orientation of complete bacterial genomes
Grupo Estudo Bioinformatica
⭐
22
Repositório do grupo de estudo de Bioinformática da rede de comunidades das PyLadies Brasil.
Macse_v2_pipelines
⭐
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.
Tiptoft
⭐
20
Predict plasmids from uncorrected long read data
Nb_distribution
⭐
20
novoBreak: local assembly for breakpoint detection in cancer genomes
Gff3toembl
⭐
20
Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
Kgwasflow
⭐
19
kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
Reactomepy
⭐
19
Explore biomolecular pathways in Reactome from the command-line or a Python script
Workflows
⭐
18
Bioinformatics curated workflows that use Biocontainers tools
Cookiecutter
⭐
18
DEPRECIATED! Please use nf-core/tools instead
Pipeline Example
⭐
18
example ruffus pipeline
Rnaseq Pipeline
⭐
18
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
Looper
⭐
18
A job submitter for Portable Encapsulated Projects
Genomedisco
⭐
18
Software for comparing contact maps from HiC, CaptureC and other 3D genome data.
Hicstuff
⭐
17
Simple library/pipeline to generate and handle Hi-C data.
Make_lastz_chains
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17
Portable solution to generate genome alignment chains using lastz
Fyrd
⭐
17
Submit functions and shell scripts to torque and slurm clusters or local machines using python.
Nf Gwas Pipeline
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17
A Nextflow Genome-Wide Association Study (GWAS) Pipeline
Igdiscover Legacy
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17
Analyze antibody repertoires and discover new V genes from high-throughput sequencing reads
Pipernaseq
⭐
16
A comprehensive pipeline for RNAseq data analysis
Metasub_cap
⭐
16
A comprehensive pipeline for short read metagenomic data
Plasmidtron
⭐
16
Assembling the cause of phenotypes and genotypes from NGS data
Cd4 Csaw
⭐
15
Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set
Sentieon Dnaseq
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15
Sentieon DNAseq
Daylily
⭐
15
A NGS analysis framework for WGS data, which automates the entire process of spinning up AWS EC2 spot instances and processing FASTQ to snvVCF in <60m, for dollars a sample and achieving Fscores of 0.998.
Bio Tradis
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15
A set of tools to analyse the output from TraDIS analyses
Tes_genes_relationship_pipeline
⭐
15
Distribution of TEs and their relationship to genes in host genome
Meta Proteome Analyzer
⭐
14
MetaProteomeAnalyzer (MPA) software for analyzing and visualizing MS-based metaproteomics data.
Seroba
⭐
14
k-mer based Pipeline to identify the Serotype from Illumina NGS reads
Mlst_check
⭐
14
Multilocus sequence typing by blast using the schemes from PubMLST
Saffrontree
⭐
14
SaffronTree: Reference free rapid phylogenetic tree construction from raw read data
Sc2 Illumina Pipeline
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14
Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub
Streamformatics
⭐
13
Real-time species-typing visualisation for nanopore data.
Edgecase
⭐
13
A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, and for haplotype inference.
Drug Sniffer
⭐
13
Sniffing out new drugs
Virmet
⭐
13
Set of tools for viral metagenomics.
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