This repository gathers pipeline-like repositories published under the AGENslab and digenoma-lab GitHub organizations.
This file is generated automatically by scripts/update_readme.py using the GitHub API. If GH_ORG_READ_TOKEN is configured, private repositories from the tracked organizations are included as well.
The GitHub Actions workflow .github/workflows/update-readme.yml refreshes it on a schedule and can also be triggered manually.
- Version: extracted from GitHub releases, tags,
nextflow.config,pyproject.toml,setup.py, or theREADMEwhen available. - Status: inferred from repository structure and explicit notes in the
README.Activeindicates an executable pipeline with workflow and documentation;In development, a pipeline under construction;Documented, a repository with documentation or associated analysis;Experimental, auxiliary material, a demo, or a template. - Tools: summarized from the
README, manifests, and the main project files detected at the repository root.
| Pipeline Name | Latest Version | Status | Description | Tools Used |
|---|---|---|---|---|
| Basecalling | 0.0.1 | Active | This Nextflow pipeline performs Nanopore basecalling using Dorado and downstream sequence statistics with SeqKit. It supports both FAST5 and POD5... | Nextflow, Dorado, Pod5 Tools, SeqKit, Slurm |
| BrumiR-Fungi | v1 | Active | Pipeline para la identificación de miRNAs candidatos en hongos a partir de datos FASTQ. | Nextflow, fastp, BrumiR, Slurm |
| mask2braker | 0.1.0 | Active | Este repositorio contiene un pipeline desarrollado en Nextflow para el análisis, anotación y evaluación de genes en genomas de novo. El flujo de... | Nextflow, windowmasker, BRAKER3, BUSCO, UniProt |
| miR-DE-cancer | No declared version | Documented | Este repositorio contiene un flujo de trabajo desarrollado en RStudio para el análisis de expresión diferencial de microRNAs (miRNAs) en proyectos... | RStudio, R, edgeR, multiMiR |
| MiRScout | 0.1.1 | Active | MiRScout is a Nextflow DSL2 pipeline for miRNA candidate discovery using dual trimming strategies and BrumiR-based prediction. | Nextflow, fastp, cutadapt, BrumiR, Random Forest |
| nextflow-template | 0.1.0 | Experimental | Este pipeline es un template mínimo de Nextflow DSL2 con módulos, workflows y un archivo principal. Solo utiliza echo para mostrar cómo fluyen los... | Nextflow, Slurm |
| nf-assembly | v1.0.0 | Active | nf-assembly is a modular pipeline built with Nextflow DSL2, designed for genome assembly, scaffolding, and annotation — particularly suited for... | Nextflow, Slurm, Hifiasm, RagTag, GFAtools |
| nf_rna_align | 1.0.0 | Active | Este pipeline automatiza las etapas de preprocesamiento, alineamiento y cuantificación de lecturas largas de RNA-seq. Está desarrollado en... | Nextflow, fastp, Slurm, BWA, FastQC |
| Prediccion-de-interacciones-miRNA-mRNA | No declared version | Documented | Este repositorio contiene el código desarrollado para una tesis que implementa y evalúa modelos de Deep Learning orientados a predecir... | Keras, Transformer |
| Python_learning-Sesion_1 | No declared version | Experimental | Fecha: 22/08/2025 Docentes: Dra. Carol Moraga e Ing. Felipe Gómez | Python |
| sarcopipe | 0.1.1 | Active | Sarcopipe is a Nextflow pipeline designed for the identification and linkage of miRNAs and mRNAs, specifically tailored for analyzing Sarcopenia... | Nextflow, fastp, BrumiR, Slurm, miRDeep2 |
| StressPathways | No declared version | Documented | identification of participant genes in different stress pathways | Not specified |
| Pipeline Name | Latest Version | Status | Description | Tools Used |
|---|---|---|---|---|
| alndv | v1.0 | Active | A nextflow (DSL 2) Whole‑Genome Short‑Read Pipeline (BWA‑MEM2 → DeepVariant → GLnexus) for small‑variant discovery from paired‑end FASTQ files. | Nextflow, Slurm, BWA, FastQC, Samtools |
| alndvs | No declared version | Documented | Somatic point mutation calling for matched and tumor-only samples | Not specified |
| alnsl | V0.1 | Active | A nextflow pipeline for alignment of short WGS reads. | Nextflow, Slurm, BWA, FastQC, Samtools |
| analisis-paper-cancer | No declared version | Documented | R code | Not specified |
| AncestryInference | 0.0.1 | Active | Nextflow pipeline for global and local ancestry inference, with QC and visualisation of the correlation between local (LAI) and global (GAI)... | Nextflow, Slurm, bcftools |
| AncestryPCA | 1.0 | Active | Ancestry PCA pipeline for genomic data, with a focus on Chilean cohorts and population-structure work alongside a reference panel (for example... | Nextflow, Slurm, bcftools |
| annotsv | 1.0 | Active | Sotfware to annotate human structural variants | Nextflow, Slurm |
| assemblies | No declared version | Documented | Repository with documentation in Rmarkdown for genome assemlies | R |
| bhap | 0.1.0 | Documented | bhap is a Bayesian classifier designed to assign haplotype labels (A, B, or U) to genomic reads based on k-mer count data. It models k-mer... | Python |
| biomining_mags | No declared version | Documented | Analysis of eight metagenomic samples sequenced via Illumina (short reads), obtained from the Cauquenes copper tailing (located in central Chile),... | Nextflow, fastp, BWA, Bakta |
| biomining_metagenomes | No declared version | Documented | Repository that holds data, scripts and figures regarding to the mining MAGs (Cauquenes tailing) article: "Genome-resolved metagenomics and... | Nextflow, BWA, CheckM, Samtools |
| BRCA | v1.0 | Active | A Nextflow pipeline for processing target NGS BRCA data | Nextflow, BWA, FastQC, Samtools, Qualimap |
| BRCA12_ms | v1.0 | Documented | Code for figure and analysis of BRCA12 ms | Nextflow |
| breast_cancer | No declared version | Documented | repo holding files for the analysis of 120 WGS of breast cancer patients | Not specified |
| call_snv | 1.0 | Active | Nextflow pipeline for the identification of Single Nucleotide Variants (SNVs) from short-read sequences. | Nextflow, Python, Slurm, Manta, Samtools |
| cancer_histology | No declared version | Experimental | Unlike genomic information, histological images of cancer patients are a simpler method of obtaining information. In particular, H&E method images... | Not specified |
| CHI-DT | No declared version | Documented | Data Note paper of Chilean genomes | Not specified |
| CHI-T2T | No declared version | Documented | Repo with analysis and data for the human genome paper. | Not specified |
| covid_genomics | v1.0 | Documented | Repository holding analysis of 100 covid chilean genomes | Not specified |
| CRAB-MIL | v1.0 | Experimental | This repository reproduces the results in the paper. | Python |
| data-TARA | No declared version | Documented | Repositorio de análisis integrados MetaTranscriptómica (MetaT), MetaGenómica (MetaG) y Taxonomía del proyecto TARA Chile. Contiene los objetos... | RStudio |
| DGL_TAT | No declared version | Documented | Repositorio con diversa documentación de procesos ejecutados por el digenoma lab en distintos cluster de computo | Not specified |
| dgl_workflows | No declared version | Documented | Repo with documentation about the different workflows of digenomalab | Bakta |
| DifferentialMethylationRegions | 0.0.1 | Active | Nextflow pipeline to preprocess modkit-style BEDs, build common CpG sets per chromosome, run differential methylation (DSS, multi-factor) and... | Nextflow, R, Slurm, bcftools, bedtools |
| dipdiff-nf | 1.0 | Active | Nextflow for running dipdiff | Nextflow, STAR, Wengan, minimap2, Samtools |
| EpiTractor | 0.1.0 | Documented | EpiTractor, a library for ancestry-based methylation DMLs. | Python |
| Eval-RF-hap | v1.0.0 | Active | Eval-RF-hap is a Nextflow pipeline designed to evaluate the haplotyping performance of RFhap (or whatever other model to separate haplotypes),... | Nextflow, Slurm, Hifiasm, Nanopore |
| EWAS | No declared version | Documented | Epigenetic wide association study | Not specified |
| fast_hybrid_polising | 0.1 | Active | nextflow run main.nf --long_reads ./test/long-reads --short_reads ./test/short-reads --outdir results --debug true | Nextflow, Slurm, Racon, minimap2 |
| FastKM | v1.0 | Documented | FastKM is a lightweight C++ tool for fast k-mer marker lookup in long reads using a minimal perfect hash function (MPHF) and a compact... | Not specified |
| fchims | No declared version | Documented | Github with code for aseembly, annotation, methylation and variants. | Not specified |
| functional_enrichment | 0.0.1 | Active | This pipeline performs functional enrichment analysis using GWAS data and local references. | Slurm, bcftools |
| Gallbladder_WGS | No declared version | Documented | Figures and analysis for Gallbladder manuscript | PURPLE |
| genome_assembly_tools | No declared version | Documented | Scripts to manipulate files associated to genome assembly | Not specified |
| GWAS | 1.6 | Active | Nextflow pipeline for genome-wide association analysis and ancestry-stratified GWAS with Tractor. Global and local ancestry (ADMIXTURE + RFMix)... | Nextflow, Slurm, Samtools, bcftools |
| hapdup-nf | v1.0 | Active | Nextflow pipeline for running HapDup for haplotype assembly. | Nextflow, STAR, Wengan, minimap2, Samtools |
| HBW | No declared version | Documented | HBW is a repository hold code for implementing trio-based binning and bubble graph approaches to diploid assembly but for hybrid genomic datasets... | Wengan |
| HistologyFeatureExtraction | 1.1 | Active | A Nextflow pipeline for extracting features from histology whole slide images (WSI) using multiple patch and slide encoders via TRIDENT. | Nextflow, Python, Slurm, OpenCV, PyTorch |
| HistologyLinearProbing | 1.4 | Active | Linear probing pipeline for histopathology to evaluate different feature extractors (foundation models) using Elastic Net classification on genes... | Nextflow, Python, R, Slurm, scikit-learn |
| HistologyMultiInstanceLearning | 1.1 | Experimental | Multi-Instance Learning (MIL) pipeline for histopathology to evaluate different MIL architectures (ABMIL, CLAM, DSMIL, etc.) using pre-extracted... | Nextflow, Python, Slurm, Transformer |
| HistoMILTrainer | 1.2 | Experimental | A library for training Multi-Instance Learning (MIL) architectures from MIL-Lab on histology datasets. HistoMILTrainer provides a unified... | Python, Slurm, PyTorch, scikit-learn, Transformer |
| hrr_analisis_er | No declared version | Documented | Description er | Not specified |
| HRR_histology | v1.0.0 | Documented | This project contains a descriptive analysis of breast biopsy data from the Hospital Regional de Rancagua. The workflow includes data cleaning,... | R |
| ImputeVariants | v1.1 | Active | ImputeVariants is a comprehensive Nextflow pipeline for genotype phasing and imputation using state-of-the-art methods. The pipeline supports two... | Nextflow, Slurm, bcftools |
| just_align_sr | 1.0 | Active | Just Align SR is a lightweight Nextflow pipeline designed for aligning short-read sequencing data (e.g., Illumina or MGI) using BWA-MEM. The... | Nextflow, Slurm, BWA, FastQC, Samtools |
| k-count-nf | 1.0 | Active | A nextflow pipeline to count k-mers and estimate genome size from WGS data | Nextflow, STAR |
| liftover | v1.2 | Active | A Nextflow pipeline for lifting over genomic coordinates from one reference genome to another (e.g., hg19 to hg38 or vice versa). Supports both... | Nextflow, Slurm, Samtools, bcftools |
| LLM-RAG-Demo | v1.1 | Experimental | Chat system for genetic variants using RAG with Milvus Lite and DeepSeek. | Python |
| longcall | 0.0.1 | Active | Longcall is a Nextflow DSL2 pipeline for Oxford Nanopore (ONT) whole-genome data that | Nextflow, Slurm, minimap2, Samtools, bcftools |
| longreadstats | v1.1 | Active | digenoma-lab/longreadstats is a bioinformatics best-practice analysis pipeline for computing long-read statistics with Nanoplot. | Nextflow, Python, Slurm |
| LRnaseq_Rat | No declared version | Documented | Repository with analysis of trascriptome data generated with Oxford Nanopore | Python, RStudio, R, Nanopore |
| MAG_ONT | No declared version | Documented | Chron metagenomic analysis of ONT data | Not specified |
| mesomic_data_note | No declared version | Documented | Repository with code and datasets used in the mesomics data note manuscript. | Not specified |
| methont | 0.1 | Active | The methont pipeline is designed to process long-read sequencing data for DNA methylation analysis. It includes alignment, variant calling,... | Nextflow, Slurm, minimap2, Samtools |
| MethylationPCA | 0.0.1 | Active | Pipeline Nextflow para preprocesar archivos BED de metilación de CpG y ejecutar un análisis de componentes principales (PCA) sobre la matriz de... | Nextflow, R, Slurm |
| minibusco-nf | V0.1 | Active | A simple and scalable Nextflow pipeline to compute genome or transcriptome quality metrics using minibusco. This pipeline is designed for... | Nextflow, BUSCO, Slurm |
| mitoH | 7.505 | Documented | Mitocondrial genome analysis | Samtools |
| mocancer | No declared version | Documented | Multi-omic analysis of cancer data | Not specified |
| nf-bakta | v1.1 | Active | A Nextflow pipeline for the annotation of bacterial genomes or MAGs running Bakta. | Nextflow, Python, UniProt, Slurm, Bakta |
| nf-groot | No declared version | Active | A Nextflow pipeline for running Groot, which is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples. | Nextflow, Slurm |
| nf-mag-depths | No declared version | Active | A nextflow pipeline to calculate depth of coverage from a metagenomic set of bins. | Nextflow, BWA, MetaBAT, Samtools |
| nf-mutect2 | v1.0 | Active | Somatic SNV/indel calling with GATK Mutect2 for WGS (hg38), including optional Panel of Normals (PON), scatter/gather sharding, and filtering.... | Nextflow, Slurm, BWA, FastQC, GATK |
| nf-ssvsr | v1.1 | Active | Simplified local Nextflow DSL2 workflow for | Nextflow, Python, Slurm, BWA, GATK |
| nf-wengan | No declared version | Documented | A nexflow workflow for wengan | Wengan |
| oncovirus | No declared version | Documented | prediction of somatic virus integration from WGS using hmftools | Not specified |
| ontmeth-nf | No declared version | Active | Nextflow pipeline to compute methylation from Nanopore data | Nextflow, Python, BWA, Samtools, Nanopore |
| ontpolish | No declared version | Documented | Polishing long-read assemblies | Not specified |
| Phasing | 1.1 | Active | A Nextflow pipeline for phasing unphased genotype data using Beagle with reference panels from the 1000 Genomes Project. | Nextflow, Slurm, Samtools, bcftools |
| qualimap-nf | 1.0 | Active | The Qualimap pipeline processes sequencing data in a fast and efficient manner using Nextflow, a workflow management system. It takes aligned... | Nextflow, Python, Slurm, Samtools, Qualimap |
| quant_mags | No declared version | Active | Quantify MAGs abundance (metaG) and gene expression (metaT) | Nextflow, Python, R |
| quantmetaT | No declared version | Active | Quantifies paired-end metatranscriptome reads using Salmon and outputs merged TPM and raw count matrices for all samples. | Nextflow, Slurm |
| RF-mut-tumor-only | No declared version | Documented | El llamado de variantes con muestras pareadas de tejido tumoral y normal es más confiable que el llamado de variantes con muestras de tumor... | RStudio, R, bcftools |
| rfhap | V2.0 | Active | A Nextflow pipeline for long-read phasing in trio datasets, leveraging multiple k-mers and a random forest classifier. | Nextflow, Random Forest, Slurm, Hifiasm |
| rfhap_ms | v1.0 | Documented | Figures and analysis for RFHAP manuscript | Not specified |
| SMAGdb | No declared version | Documented | The soid metagenome data base and analysis toolkit | Not specified |
| snps_mags | V1.0 | Active | snps_mags is a Nextflow pipeline designed for calling point mutations in Metagenome-Assembled Genomes (MAGs) using InStrain. The pipeline... | Nextflow, Slurm, BWA, FastQC, Samtools |
| somalier-nf | v1.0 | Active | Minimal Nextflow DSL2 pipeline for somalier, the pipeline include | Nextflow, Slurm, somalier |
| somatic_point_mutations | v1.1 | Active | This repository provides a Nextflow pipeline for calling somatic point mutations from tumor/normal pairs using Whole Genome Sequencing (WGS) or... | Nextflow, Python, Slurm, Manta, bcftools |
| SomaticVariantCalling | 0.0.1 | Active | A Nextflow (DSL 2) pipeline that takes pre‑aligned whole‑genome CRAM files and runs DeepVariant (autosomes only) followed by GLnexus cohort merging. | Nextflow, Slurm, Qualimap |
| spg | 1.0 | Active | Simple Pan-Genome workflow for MAGs. | Nextflow, Python, Slurm, MetaBAT, Prokka |
| Summer_Course_ML | No declared version | Experimental | Material for the CMM summer course | Not specified |
| SV_Delly_Germline | 1.0 | Active | This pipeline identifies germline structural variants (SVs) — deletions, duplications, inversions, insertions, and translocations — from... | Nextflow, Slurm, Delly, bcftools |
| svlr | 1.0 | Active | A nextflow Structural variant calling workflow for long-reads | Nextflow, Slurm, minimap2, Samtools |
| svlr_somatic | 1.0 | Active | A Nextflow pipeline for somatic structural variant (SV) calling using long-read sequencing data. | Nextflow, Slurm, minimap2, Samtools |
| systemix_mag_analysis | No declared version | Documented | Repository holding analysis and figures to understand MAG (Metagenome-Assembled Genome) data. | Nextflow, RStudio, CheckM, Bakta, Prokka |
| TARA-Chile | No declared version | Documented | Genomics of TARA Ocean Chile expedition | Not specified |
Note: this table is heuristic. Some repositories do not declare versions or toolchains explicitly, so the best possible inference is shown from the metadata available on GitHub.