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Search results for pipeline genomics
genomics
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pipeline
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80 search results found
Galaxy
⭐
1,211
Data intensive science for everyone.
Scrna Seq_notes
⭐
478
A list of scRNA-seq analysis tools
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
Flowcraft
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234
FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦
Aws Batch Genomics
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181
Software sets up and runs an genome sequencing analysis workflow using AWS Batch and AWS Step Functions.
Gatk Sv
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148
A structural variation pipeline for short-read sequencing
Cloud Pipeline
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137
Cloud agnostic genomics analysis, scientific computation and storage platform
Viral Ngs
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129
Viral genomics analysis pipelines
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.
Scrnaseq
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119
A single-cell RNAseq pipeline for 10X genomics data
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
Hgtector
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87
HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.
Callings Nf
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76
GATK RNA-Seq Variant Calling in Nextflow
Rnaseq Nf
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59
A proof of concept of RNAseq pipeline
Pipelines Api Examples
⭐
46
Examples for the Google Genomics Pipelines API.
Bio Pipeline
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45
My collection of light bioinformatics analysis pipelines for specific tasks
Bactmap
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45
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
Allhic
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41
Genome scaffolding based on HiC data in heterozygous and high ploidy genomes
Get_phylomarkers
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39
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
Genomics Secondary Analysis Using Aws Step Functions And Aws Batch
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38
This solution provides a framework for Next Generation Sequencing (NGS) genomics secondary-analysis pipelines using AWS Step Functions and AWS Batch.
Dnapipete
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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).
Dee2
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37
Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data
Gawn
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37
Genome Annotation Without Nightmares
Dataflow Java
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35
Google Cloud Dataflow pipelines such as Identity-By-State as well as useful utility classes.
Mtbseq_source
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32
MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.
Circrna
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32
circRNA quantification, differential expression analysis and miRNA target prediction 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
Toil Scripts
⭐
30
Toil workflows for common genomic pipelines
Cpipe
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29
The open source version of the Melbourne Genomics Health Alliance Exome Sequencing Pipeline
Pgcgap
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29
The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline
Busco_phylogenomics
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26
BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins
Genipe
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26
Genome-wide imputation pipeline
Phylociraptor
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23
rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference
Pipelines Tools
⭐
23
Tools for developing and running pipelines with the Genomics API
Mapache
⭐
23
mapping pipeline for ancient DNA
Sv Pipeline
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21
Pipeline for structural variation detection in cohorts
Spandx
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20
SPANDx - Comparative genomics for next-generation haploid sequence data
Variant_catalogue_pipeline
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20
Variant catalogue pipeline
Kgwasflow
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19
kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
Companion
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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
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.
Rnaseq Pipeline
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18
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
Stackr
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17
stackr: an R package to run stacks software pipeline
Bactpipe
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17
BACTpipe: An assembly and annotation pipeline for bacterial genomics
Treeval
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17
Pipelines for the production of Treeval data
10x_snakepipe
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17
A snakemake pipeline for 10X genomics cellranger
Genomenote
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16
This Nextflow DSL2 pipeline takes aligned HiC reads, creates contact maps and a table of statistics.
Human_genomics_pipeline
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15
A Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.
Pigx
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15
Pipelines in genomics
Vsnp
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13
vSNP -- validate SNPs
Falcon Genome
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13
Falcon Accelerated Genomics Pipelines
Xpresspipe
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11
An alignment and analysis pipeline for Ribosome Profiling and RNA-seq data
Deepvariant On Spark
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11
DeepVariant-on-Spark is a germline short variant calling pipeline that runs Google DeepVariant on Apache Spark at scale.
Exoseq
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10
Please consider using/contributing to https://github.com/nf-core/sarek
Isb Cgc Pipelines
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10
Framework for running bioinformatic workflows and pipelines using the Google Pipelines API as the underlying task-runner.
Aether
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10
Intelligent and cost-effective bidding on cloud computing instances for bioinformatics pipelines.
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
Banzai Microbialgenomics Pipeline
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10
Banzai is a Microbial Genomics Next Generation Sequencing (NGS) Pipeline Tool developed within Dr Scott Beatson’s Group at the University of Queensland
Rmghc 2018
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10
Nextflow Workshop at Rocky Mountain Genomics HackCon 2018
Polishclr
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10
A nextflow pipeline for polishing CLR assemblies
Blobtoolkit
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9
Nextflow pipeline for BlobToolKit for Sanger ToL production suite
Arks
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9
🌈Alignment-free scaffolding of genome assemblies with 10x Genomics Chromium reads
Multiphate2
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8
multiPhATE with comparative genomics
Snakemake_rnaseq
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8
A Snakemake pipeline to go from fastq mRNA sequencing files to raw and normalised counts (usable for downstream EDA and differential analysis)
Bigquery Genomics Qc
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7
Genomics QC pipeline
Mgp1000
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7
Nextflow bioinformatics pipeline for large-scale analysis of Multiple Myeloma genomes
Scanpav
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7
Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.
Fastdtlmapper
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7
Genome-wide gene gain/loss mapping tool using DTL(Duplication-Transfer-Loss) reconciliation method
Hybkit
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6
Toolkit for analysis of ".hyb" format nucleotide sequence data from chimeric RNA experiments.
Gps Pipeline
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6
Nextflow Pipeline for processing Streptococcus pneumoniae sequencing raw reads (FASTQ files) by the GPS Project (Global Pneumococcal Sequencing Project)
Cg Pipeline
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6
Genome assembly/prediction/annotation pipeline for the Linux command line
Rna Seq
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6
bioinformatics pipelines
Readmapping
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6
Nextflow DSL2 pipeline to align short and long reads to genome assembly. This workflow is part of the Tree of Life production suite.
Genomeassembly
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5
Implementation of ToL genome assembly workflows
Nf Repeatmasking
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5
Nextflow workflow for automatic repeat detection, classification and masking
Ngi Nextflowdocs
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5
Common documentation for National Genomics Infrastructure pipelines built with Nextflow
Eager Gui
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5
The EAGER Pipeline
Allmine
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5
AllMine, a flexible pipeline for Allele Mining. Develloped at INRA's GAFL unit :
Recenthgt
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5
A novel bioinformatics pipeline for recent horizontal gene transfer detecting.
Ipsa Nf
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5
Integrative Pipeline for Splicing Analyses (IPSA) in Nextflow
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