OpenOmics

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48 repositories

chrom-seek
Public
An awesome set of epigenetic pipelines for bulk cfChip-seq, ChIP-seq, and ATAC-seq
quality-control annotation chip-seq atac-seq bulk cell-free-dna peak-calling differential-accessibility differential-binding
Python
•
MIT License
•2•5•8•2•Updated Jul 30, 2025Jul 30, 2025
methyl-seek
Public
Bisulphite-sequencing DNA methylation pipeline
Python
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MIT License
•3•7•2•1•Updated Jul 23, 2025Jul 23, 2025
genome-seek
Public
Clinical Whole Genome and Exome Sequencing Pipeline
quality-control snakemake pipeline somatic-variants singularity copy-number-variation whole-exome-sequencing whole-genome-sequencing variant-annotation hla-typing
Python
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MIT License
•10•23•5•0•Updated Jul 22, 2025Jul 22, 2025
cell-seek
Public
One single-cell pipeline to rule them all, one pipeline to find them, one pipeline to unify them all, and with the data bind them.
10xgenomics single-cell-rna-seq single-cell-atac-seq single-cell-omics single-cell-vdj single-cell-cite-seq
Python
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MIT License
•1•1•0•0•Updated Jul 22, 2025Jul 22, 2025
ervx
Public
Endogenous Retrovirus Expression Pipeline for Human, Mouse, and Macaque for use with bulk RNA-seq
workflow quality-control snakemake pipeline human mouse singularity herv transposable-elements endogenous-retrovirus-expression
Python
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MIT License
•1•1•2•0•Updated Jul 17, 2025Jul 17, 2025
scribble
Public
Scripts/code-snippets, somewhere in-between bioinformatics and data science, and oneliners
Python
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MIT License
•3•4•0•0•Updated Jul 14, 2025Jul 14, 2025
metamorph
Public
Metagenomics and Metatranscriptomics pipeline
quality-control snakemake pipeline metagenomics metatranscriptomics
Python
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MIT License
•1•5•4•0•Updated Jul 14, 2025Jul 14, 2025
space-seek
Public
Spatial-sequencing: The final frontier. These are the voyages of the 10x Visium pipeline, space-seek.
snakemake pipeline singularity single-cell 10xgenomics visium-hd
Python
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MIT License
•0•1•0•0•Updated Jul 11, 2025Jul 11, 2025
RNA-seek
Public
A comprehensive quality-control and quantification RNA-seq pipeline
Python
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MIT License
•13•4•0•0•Updated Jul 9, 2025Jul 9, 2025
leafworker
Public
An awesome snakemake pipeline to run leafcutter and IsoformSwitchAnalyzeR.
Python
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MIT License
•0•1•3•0•Updated Jun 26, 2025Jun 26, 2025
mpox-seek
Public
A rapid pipeline for targeted and whole-genome ONT monkeypox sequencing
snakemake pipeline conda rapid singularity phylogenetics oxford-nanopore mamba monkeypox mpox
Python
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MIT License
•0•1•0•0•Updated May 20, 2025May 20, 2025
weave
Public
An awesome BCL demultiplexing and FastQ quality-control pipeline
kaiju bcl2fastq fastp krona kraken2 bclconvert fastq-quality-control contamination-screening disambiguate-genomes
Python
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MIT License
•0•1•6•1•Updated Apr 22, 2025Apr 22, 2025
profiles
Public
A universal set of snakemake profiles for different clusters at the NIH
Python
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MIT License
•0•2•0•0•Updated Apr 15, 2025Apr 15, 2025
nanite
Public
A streamlined Oxford Nanopore Viral Metagenomics Pipeline
snakemake annotation assembly slim singularity classification viral-metagenomics pathogen-surveillance pipeline
Python
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MIT License
•2•4•1•0•Updated Mar 27, 2025Mar 27, 2025
mr-seek
Public
Mendelian Randomization pipeline
snakemake mendelian-randomization pipeline
Python
•
MIT License
•1•2•0•0•Updated Mar 27, 2025Mar 27, 2025
snakevision
Public
An awesome tool to visualize snakemake rule graphs
visualization snakemake networkx dag dot-graphics rulegraph dagviz
Python
•
MIT License
•0•13•1•0•Updated Mar 26, 2025Mar 26, 2025
baseline
Public template
A BASE template for building pipeLINEs
snakemake pipeline-template
Python
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MIT License
•1•3•1•0•Updated Mar 18, 2025Mar 18, 2025
cyte-seek
Public
Awesome single-cell CITE-sequencing Pipeline
quality-control singularity single-cell 10xgenomics cite-seq pipeline
Python
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MIT License
•0•2•0•0•Updated Mar 17, 2025Mar 17, 2025
metavirs
Public
Viral Metagenomics Assembly and Annotation Pipeline
quality-control snakemake annotation assembly singularity classification viral-metagenomics pathogen-surveillance pipeline
Python
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MIT License
•1•5•3•0•Updated Mar 17, 2025Mar 17, 2025
pbAmp-seek
Public
Identify and count PacBio Hifi amplicons
Python
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MIT License
•2•1•0•0•Updated Mar 17, 2025Mar 17, 2025
scErvx
Public
Endogenous Retrovirus Expression Pipeline for Human and Mouse for use with data from 10x genomics (bam files)
single-cell-rna-seq endogenous-retrovirus-expression
Python
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MIT License
•0•1•0•0•Updated Mar 17, 2025Mar 17, 2025
parabricks-benchmark
Public
Benchmarking parabricks GPU-accelerated tools for GATK and beyond!
Python
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MIT License
•0•1•0•0•Updated Mar 17, 2025Mar 17, 2025
mir-seek
Public
An awesome microRNA-sequencing pipeline
snakemake singularity mirna mirdeep2 mirna-seq micro-rna micro-rna-expression mature-mirna
Python
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MIT License
•1•2•2•0•Updated Mar 17, 2025Mar 17, 2025
modr
Public
An awesome Oxford Nanopore Pipeline for direct RNA-sequencing
bioinformatics quality-control pipeline singularity alternative-splicing-analysis transcriptomics oxford-nanopore rna-editing differential-expression-analysis snakemake-pipeline
Python
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MIT License
•1•5•2•0•Updated Mar 17, 2025Mar 17, 2025
istari
Public
Perform error-prone data preparation for whole genome regression modeling
Python
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MIT License
•1•1•0•0•Updated Mar 17, 2025Mar 17, 2025
assembly-seek
Public
De novo Long-read Genome Assembly Pipeline
Python
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MIT License
•2•2•4•0•Updated Mar 17, 2025Mar 17, 2025
HiIP
Public
An awesome Hi-C + ChIP (HiChIP) sequencing pipeline.
snakemake pipeline singularity hi-c chip-seq hichip
Python
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MIT License
•0•0•1•0•Updated Mar 17, 2025Mar 17, 2025
dockerfiles
Public
Dockerfiles for reproducible scientific research and beyond!
Python
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MIT License
•1•0•0•0•Updated Mar 12, 2025Mar 12, 2025
SnakeMaker
Public
A repository for the Maker Snakemake pipeline
Python
•2•0•0•0•Updated Feb 18, 2025Feb 18, 2025
SnakeMaker_alt
Public
A repository for the Maker Snakemake pipeline
Python
•2•0•0•0•Updated Jan 24, 2025Jan 24, 2025