GitHub topics: snakemake-workflow

Repositories

felixleopoldo/benchpress

Scalable open-source software to run, develop, and benchmark causal discovery algorithms

Language: Python - Size: 124 MB - Last synced at: about 22 hours ago - Pushed at: 1 day ago - Stars: 74 - Forks: 20

refmyoussef-source/mdr-pa-genomic-epidemiology

A reproducible Snakemake pipeline for the high-throughput genomic epidemiology of 96 MDR P. aeruginosa strains (BioProject PRJNA771342).

Language: Jupyter Notebook - Size: 370 KB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 1 - Forks: 0

RIVM-bioinformatics/ViroConstrictor

ViroConstrictor is a pipeline designed to process raw FastQ data from viral amplicon-based sequencing and generate biologically correct consensus sequences of the given viral genome

Language: Python - Size: 3.22 MB - Last synced at: about 17 hours ago - Pushed at: about 20 hours ago - Stars: 7 - Forks: 2

fischuu/Pipeline-Holoruminant-Meta

Easy to use Snakemake metagenomic pipeline that covers a) read-based analysis b) contig based analysis and c) MAG assembly and annotation using a broad set of ready to use and included public databases and annotators

Language: HTML - Size: 25.3 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 6 - Forks: 0

LucvZon/nanopore-amplicon-analysis-manual

This is a manual for viral amplicon data analysis of Nanopore long reads

Language: Python - Size: 693 KB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 0 - Forks: 0

LucvZon/LoViMAB

Long-Read Viral Metagenome Assembly Benchmark (LoViMAB) is a pipeline made to compare metagenomic assemblies of viral nanopore reads.

Language: Python - Size: 113 KB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 0 - Forks: 0

ryguy2k4/studytime

Analysis of my time spent studying at UIUC.

Language: Jupyter Notebook - Size: 14.4 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 0 - Forks: 0

arcxteam/arcxteam

Code for Fun, Let's Me See my Github Profile - Readme Stats :octocat::octocat:

Size: 7.14 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 5 - Forks: 0

akbaritabar/Replication-package-for-gender-and-regional-differences-in-scientific-mobility-and-immobility

Scripts, data, and replication materials for "A study of gender and regional differences in scientific mobility and immobility among researchers identified as potentially talented"

Language: HTML - Size: 25.9 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 1 - Forks: 0

niekwit/crispr-screens

Snakemake workflow for CRISPR-Cas9 screen analysis

Language: Python - Size: 35.7 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 7 - Forks: 1

niekwit/gps-orfeome

GPSW: A Snakemake workflow for GPS-ORFeome screens

Language: Python - Size: 101 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 4 - Forks: 0

EchoSingh/EchoSingh

This repository serves as the foundation of my GitHub profile README, highlighting my projects, technical skills, and professional journey. It provides an overview of my contributions to open-source, personal projects, and areas of interest, while also reflecting my commitment to continuous learning and innovation.

Size: 16.8 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 4 - Forks: 3

ylab-hi/ScanNeo2

Snakemake-based computational workflow for neoantigen prediction from diverse sources

Language: Python - Size: 37.8 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 13 - Forks: 1

Nirmal2310/ANOMALY

Snakemake workflow for calling NUMTs from Long read sequencing data. The pipeline takes either FASTQ or BAM file and outputs a text file containing NUMTs.

Language: Shell - Size: 5.61 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 4 - Forks: 0

Serka-M/mmlong2-lite

Lightweight bioinformatics pipeline for microbial genome recovery

Language: Python - Size: 1.46 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 17 - Forks: 3

niekwit/damid-seq

DamMapper: Snakemake workflow for DamID-Seq analysis

Language: Python - Size: 83.3 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 4 - Forks: 0

4dn-dcic/tibanna

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.

Language: Python - Size: 134 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 71 - Forks: 28

guigolab/LyRic

Long RNA-seq analysis workflow

Language: Python - Size: 76.3 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 20 - Forks: 5

s-shemmee/s-shemmee

Config files for my GitHub profile.

Size: 2.71 MB - Last synced at: about 4 hours ago - Pushed at: about 5 hours ago - Stars: 19 - Forks: 10

allytrope/variant-analysis

A Snakemake pipeline for variant calling of genomic FASTQ data using GATK

Language: Jupyter Notebook - Size: 4.46 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 5 - Forks: 0

tucca-cellag/tucca-rna-seq

TUCCA's RNA-Seq Workflow for Differential Expression and Pathway Enrichment Analysis

Language: Python - Size: 31.2 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 18 - Forks: 0

sanjaynagi/AmpSeeker

A snakemake workflow for amplicon sequencing

Language: Jupyter Notebook - Size: 108 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 2 - Forks: 4

MPUSP/snakemake-workflow-template Fork of snakemake-workflows/snakemake-workflow-template

A template for standard compliant snakemake-workflows

Language: Python - Size: 76.2 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 1

MPUSP/snakemake-simple-mapping

A Snakemake workflow for the mapping of reads to reference genomes, minimalistic and simple.

Language: Python - Size: 2.47 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

MPUSP/snakemake-ont-basecalling

A Snakemake workflow for basecalling and demultiplexing of Oxford Nanopore data using Dorado.

Language: Python - Size: 351 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 4 - Forks: 0

metagenlab/MeSS

Snakemake pipeline for simulating shotgun metagenomic samples

Language: Python - Size: 5.92 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 23 - Forks: 3

trangle1302/2D_shapespace

Language: Jupyter Notebook - Size: 80.1 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 1

niekwit/rna-seq-star-tetranscripts

Snakemake workflow for transposable element RNA-Seq using TEtranscripts

Language: Python - Size: 95.3 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 4 - Forks: 0

akbaritabar/cookiecutter_projects_template

A cookiecutter template to reuse at the start of projects.

Language: HTML - Size: 716 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

moiexpositoalonsolab/grenepipe

A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - for sampled individuals, and for pool sequencing.

Language: Python - Size: 100 MB - Last synced at: 3 months ago - Pushed at: 5 months ago - Stars: 106 - Forks: 24

ImagoXV/NanoASV

NanoASV official repo

Language: Shell - Size: 86.4 MB - Last synced at: 3 months ago - Pushed at: 6 months ago - Stars: 10 - Forks: 3

centrefornetzero/pypsa-fes

A model that optimises investment and operation, and incorporates flexibility domestic demand flexibility to model scenarios for Great Britain's future energy system.

Language: Python - Size: 99.2 MB - Last synced at: 2 days ago - Pushed at: 10 months ago - Stars: 27 - Forks: 2

rgomez-AI/3DChromTrans

Measure distances between two types of markers during FISH Assay after Chromosomal Translocation event

Language: Python - Size: 1.06 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

rgomez-AI/CellOrientation

Test of Uniformity for centrosome orientation at early timepoints during Wound Healing Assay

Language: R - Size: 48.8 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

ctglab/isoworm

A Snakemake pipeline developed to quantify isoforms expression levels in large RNA-seq datasets and find poly-A sites

Language: Python - Size: 51 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 4 - Forks: 0

varunchakrakodi/genome_alignment

Snakemake file for handling concatenated Illumina .fastq.gz files to generate aligned sequence

Language: Python - Size: 52.7 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

tdayris/fair_genome_indexer

Download and index Ensembl sequences and annotations, remove non-canonical chromosimes, remove low TSL, index with multiple tools

Language: Python - Size: 1.02 MB - Last synced at: 3 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

open2c/distiller-sm

a Snakemake version of distiller - the Open2C Hi-C mapping workflow

Language: Python - Size: 146 KB - Last synced at: 4 months ago - Pushed at: 5 months ago - Stars: 5 - Forks: 3

akbaritabar/course-session-on-Other-Computational-Social-Science-Skills

Materials for course on ""Other" Computational Social Science Skills" at the fourth MPIDR Summer Incubator Program, June 10, 2025, Rostock, Germany (and online)

Language: HTML - Size: 4.57 MB - Last synced at: 3 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0

ntnn19/AlphaFold3_workflow

A Snakemake workflow for high-throughput AlphaFold 3 structure predictions

Language: Python - Size: 321 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 3 - Forks: 0

bcgsc/IMPALA

Integrated Mapping and Profiling of Allelically-expressed Loci with Annotations

Language: R - Size: 20 MB - Last synced at: 3 months ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 0

vibaotram/baseDmux

snakemake workflow for basecalling and demultiplexing of ONT sequencing data

Language: Python - Size: 84.2 MB - Last synced at: 4 months ago - Pushed at: over 2 years ago - Stars: 7 - Forks: 1

niekwit/rna-seq-salmon-deseq2

Snakemake workflow for RNA-Seq differential transcript analysis using Salmon/Deseq2

Language: Python - Size: 317 MB - Last synced at: about 1 month ago - Pushed at: 6 months ago - Stars: 5 - Forks: 1

Zhanglab-IOZ/TnpB

Snakemake workflows for TAM depletion analysis and de novo IS605 annotation

Language: Python - Size: 36.1 KB - Last synced at: 3 months ago - Pushed at: about 1 year ago - Stars: 5 - Forks: 3

fritzbayer/snakemake-with-R

Simple template for running snakemake with R

Language: R - Size: 35.2 KB - Last synced at: about 2 months ago - Pushed at: almost 3 years ago - Stars: 12 - Forks: 1

meeranhussain/Population_genomic_analysis

A repository for efficient population genomic analysis using Snakemake workflow.

Language: R - Size: 919 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

akbaritabar/Internal-and-international-migration-of-scientists

Scripts, data, and replication materials for "Global subnational estimates of migration of scientists reveal large disparities in internal and international flows"

Language: HTML - Size: 1.17 GB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 2 - Forks: 0

ctubbs750/snakemake-genome-bottle

Snakemake workflow to install reference genomes and their supporting files

Language: Python - Size: 43.9 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 0

Swart-lab/loxodes-nucleosomes-workflow

Language: Jupyter Notebook - Size: 777 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

sanjaynagi/rna-seq-pop

Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data

Language: Jupyter Notebook - Size: 99.5 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 18 - Forks: 9

tdayris/fair_bowtie2_mapping

Align reads over a reference genome, filter aligned-reads, and mark duplicates

Language: Python - Size: 5.91 MB - Last synced at: 3 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

tdayris/fair_gatk_mutect2

Snakemake workflow used to call germline and/or somatic variants with GATK Mutect2

Language: Python - Size: 178 KB - Last synced at: 3 months ago - Pushed at: 8 months ago - Stars: 1 - Forks: 1

tdayris/fair_macs2_calling

Snakemake workflow used to call peaks with Macs2

Language: Python - Size: 3.42 MB - Last synced at: 3 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

hoomanhanaei/RNAseq_DataAanalysis

RNA Sequencing Data Analysis: A 2025 Review and Updated Snakemake Pipeline

Language: Python - Size: 21.5 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

YunanJeong/ftp-to-s3

Language: Python - Size: 41 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

ruppinlab/tcga-wgs-kraken-microbial-quant

Kraken2 + Bracken based pipeline for classifying and quantifying microbial reads from GDC TCGA WGS data

Language: Python - Size: 21.7 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 1

AngryMaciek/warlock

Warlock is a snakemake workflow to spawn multiple demons (deme-based oncology models) as jobs running around on a cluster environment 😈😈

Language: Python - Size: 284 KB - Last synced at: 2 months ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 0

elbecerrasoto/variants

Variant Calling Snakemake Pipeline

Language: Python - Size: 391 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0

kristinassong/RNAseq

A Snakemake pipeline to analyze RNA-seq expression data

Language: Python - Size: 117 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

tdayris/fair_rnaseq_salmon_quant

Snakemake workflow designed to perform RNASeq transcrpotime expression estimation with Salmon

Language: Python - Size: 183 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

CCBR/CCBR_circRNA_AmpliconSeq

Snakemake workflow to process circRNA AmpliconSeq datasets generated to study circRNAs in KSHV and human hosts using divergent primers.

Language: Shell - Size: 480 KB - Last synced at: 2 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 1

laelbarlow/amoebae

Workflow for identifying and classifying homologous gene/protein sequences

Language: Python - Size: 7.72 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 20 - Forks: 2

ThibaultLatrille/SelCoeff

Estimating the proportion of beneficial mutations that are not adaptive in mammals

Language: TeX - Size: 15.3 MB - Last synced at: about 1 month ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0

0xEtherPunk/0xEtherPunk

My GitHub profile README with contribution statistics and activity visualization.

Size: 56.6 KB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 0 - Forks: 0

IRI-UW-Bioinformatics/flu-ngs

NGS pipeline for influenza virus libraries

Language: Python - Size: 135 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 2 - Forks: 0

chazeon/dpgen-snakemake

A lightweight Snakemake-based workflow that implements the DP-GEN scheme.

Language: Python - Size: 13 MB - Last synced at: about 1 month ago - Pushed at: almost 3 years ago - Stars: 5 - Forks: 0

Moha-cm/AutoRNASeq

Simplified RNA-Seq Insights with automation

Language: HTML - Size: 4.61 MB - Last synced at: 7 months ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 1

suqingdong/FastMitoAssembler

Fast Assembler Workflow for MitoGenome

Language: Python - Size: 67.4 KB - Last synced at: 23 days ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0

ThibaultLatrille/MicMac

Detecting diversifying selection for a trait from within and between-species genotypes and phenotypes

Language: C++ - Size: 18.8 MB - Last synced at: 8 months ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

person-c/bulkRNAseq_snakemake

Snakemake workflow for bulkRNAseq

Size: 26.4 KB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

svsuresh/tuxedo2_snakemake

Language: R - Size: 192 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

andnischneider/its_workflow

Repository to process ITS amplicon sequencing data and produce figures for Schneider et al (2021)

Language: R - Size: 2.53 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 3

seqscope/NovaScope

The pipeline to process Novaseq dataset, from fastq to nge.

Language: Python - Size: 52.9 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 0

fungenomics/scCoAnnotate Fork of HusseinLakkis01/scCoAnnotate

Pipeline for consensus prediction of cell types in single-cell RNA sequencing data.

Language: R - Size: 927 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 0

WissalManseri/WissalManseri

🦄 This repository contains all the best practices about GitHub

Size: 121 KB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 1 - Forks: 0

bedapub/HBVouroboros

HBVouroboros automates sequencing-based HBV genotyping and expression profiling

Language: Python - Size: 23.6 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 1

JuanCarlosBio/RNA-Seq_VIU

Actividades de la asignatura de Análisis de transcriptómicos de la expresión génica

Language: Python - Size: 35.8 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

JuanCarlosBio/TFM

END OF MASTER'S PROJECT: Valencian International University VIU

Language: Jupyter Notebook - Size: 41.1 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

thomasbtf/document-anonymization

Personal data redaction on images based on FHIR patient resources.

Language: Python - Size: 4.1 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 4 - Forks: 0

simon-bt/sm-rnaseq-splicing

Snakemake pipeline for alternative slicing analysis with VAST-TOOLS

Language: Python - Size: 17.6 KB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

Swart-lab/loxodes-bleties-workflow

Language: Jupyter Notebook - Size: 366 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

ccaudek/snakemake_playground

Snakemake tutorial

Language: HTML - Size: 3.01 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

niekwit/cut_and_run

Snakemake workflow for Cut & Run

Language: Python - Size: 72.4 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

NovembreLab/eems-around-the-world

Repo to analyze population genetic data with many different methods

Language: R - Size: 9.92 MB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 14 - Forks: 8

RIVM-bioinformatics/SARS2seq

SARS2seq is a pipeline designed to process raw FastQ data from targeted SARS-CoV-2 sequencing and generate biologically correct consensus sequences of the SARS-CoV-2 genome.

Language: Python - Size: 1.41 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 0

pyc1216/hlaloh-pipeline

hla-typing by optitype & polysolver , detect loh by lohhla.

Language: R - Size: 6.39 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 1

zavolanlab/SCUREL

Method to detect 3'UTR changes from scRNA-seq

Language: Python - Size: 30.7 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 3 - Forks: 1

insilicoconsulting/snake-chic

Snakemake wrapper around the Arima Capture Hi-C (CHiC) workflow

Language: Python - Size: 8.79 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

meeranhussain/RNASeq_DEGseq_Snakemake_NO-REPLICATES

Workflow for differential gene expression analysis for non-replicate samples using DEGseq

Language: R - Size: 20.5 KB - Last synced at: 9 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

meeranhussain/RNASeq_Deseq2_Snakemake

Differential gene expression analysis for samples with replicates using STAR-DeSeq2 pipeline

Language: R - Size: 46.9 KB - Last synced at: 9 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

areebapatel/Rapid-CNS2 📦

Rapid comprehensive adaptive nanopore-sequencing of CNS tumours set-up and analysis pipeline

Language: Shell - Size: 572 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

Related Keywords

snakemake-workflow 128 snakemake 53 bioinformatics 29 bioinformatics-pipeline 16 python 11 conda 8 ngs-analysis 8 variant-calling 8 snakemake-pipeline 7 rna-seq-pipeline 7 workflow 6 reproducible-research 6 metagenomics 5 readme-profile 5 transcriptomics 5 genomics 5 rna-seq 4 nanopore 4 ngs-pipeline 4 multiqc 4 profile-readme 4 ngs 4 amplicon-sequencing 4 reproducible-workflows 3 nanopore-sequencing 3 salmon 3 rnaseq-pipeline 3 fair 3 snakemake-wrappers 3 population-genetics 3 readme 3 readme-template 3 fastqc 3 basecalling 3 python3 3 bowtie2 3 rna-seq-analysis 3 consensus-sequences 3 rnaseq 3 snakemake-pipelines 3 reproducibility 3 bioinformatics-workflow 3 long-read-sequencing 3 r 3 renv 2 deseq2 2 differential-expression 2 scientific-papers 2 github 2 config 2 differential-gene-expression 2 snake 2 snake-game 2 singularity 2 star-aligner 2 kallisto 2 nanopore-analysis-pipeline 2 github-config 2 docker 2 genomic-surveillance 2 pipeline 2 open-source 2 bash 2 bioimage-analysis 2 readme-md 2 hic 2 gencode 2 hi-c 2 cellprofiler-pipeline 2 workflow-automation 2 profile 2 gatk-bestpractices 2 data-science 2 covid-19-estonia 2 viral-metagenomics 2 korogeno-est 2 sars-cov-2 2 oxford-nanopore 2 parallel-computing 2 metagenome-assembled-genomes 2 snakefile 2 viruses 2 virology 2 rivm 2 public-health 2 rnaseq-analysis 2 genome-assembly 2 computational-social-science 2 cookiecutter 2 benchmarking 2 duckdb 2 similarity-search 2 population-genomics 2 next-generation-sequencing 2 scientific-mobility 2 scholarly-migration 2 loxodes 2 migration 2 international-migration 2 sambamba 2