Tag: nextflow
WGBS Pipeline: FASTQ to Methylation Calling
This skill executes the full ENCODE WGBS pipeline, processing paired-end FASTQ reads through alignment, deduplication, and methylation extraction. It generates per-CpG methylation levels in the standardized bedMethyl format, suitable for do…
ENCODE Hi-C Data Processing Pipeline
This Nextflow pipeline processes Hi-C FASTQ files to generate multi-resolution contact matrices and chromatin loop calls. It integrates BWA, pairtools, Juicer, and cooler for end-to-end chromatin conformation analysis.
ENCODE pipeline workflow generation and management
This skill facilitates the generation and execution of standardized ENCODE bioinformatics pipelines, supporting custom Nextflow or WDL workflows. It manages compute resource requirements and deployment across local, HPC, and major cloud pla…
ENCODE DNase-seq Pipeline for Hotspots and Footprints
This skill executes the comprehensive ENCODE DNase-seq pipeline, processing paired FASTQ reads to identify DNase hypersensitive sites (DHSs) and perform TF footprinting analysis. It utilizes Nextflow to generate critical data products, incl…
CUT/CUT Peak Calling Pipeline
This tool executes a comprehensive Nextflow pipeline for processing CUT or CUT FASTQ data. It handles alignment, spike-in normalization, and generates peak calls using SEACR or MACS2, producing normalized signal tracks and genomic peaks.
ENCODE ChIP-seq Analysis Pipeline for Peak Calling
This skill executes a complete, standards-compliant ChIP-seq workflow, processing raw FASTQ files through alignment, MACS2 peak calling, and IDR analysis. It generates comprehensive peak sets and signal tracks, adhering to ENCODE guidelines…
ENCODE ATAC-seq Pipeline for Chromatin Accessibility Analysis
This skill executes the comprehensive ENCODE ATAC-seq workflow, processing raw FASTQ files through alignment, Tn5 offset correction, and filtering. It generates high-quality peak calls and signal tracks suitable for detailed chromatin acces…
WGBS Pipeline: FASTQ to Methylation Calling
Executes the full ENCODE Whole Genome Bisulfite Sequencing pipeline, processing paired-end FASTQ files through alignment, deduplication, and methylation extraction. It generates comprehensive per-CpG methylation levels in the standard bedMe…
ENCODE Hi-C Processing Pipeline
Executes the ENCODE Hi-C pipeline using Nextflow to transform FASTQ files into multi-resolution contact matrices and loop calls. The pipeline supports local, SLURM, and cloud-based deployments via Docker.
ENCODE RNA-seq Quantification Pipeline
This tool executes a comprehensive, ENCODE-standard RNA-seq pipeline using Nextflow. It processes raw FASTQ data through STAR alignment, generating gene/transcript quantification (TPM/FPKM) and strand-specific bigWig signal tracks.
ENCODE Pipeline Workflow Generation and Management
This skill facilitates the generation and execution of complex ENCODE bioinformatics workflows, supporting custom Nextflow and WDL pipelines. It manages compute resource requirements and deployment across local, HPC, and major cloud platfor…
CUT and CUT Processing Pipeline
Executes a Nextflow-based pipeline for processing CUT and CUT data from FASTQ files to peaks and signal tracks. The workflow incorporates spike-in normalisation and SEACR peak calling for high-resolution chromatin profiling.
DNase-seq pipeline for accessibility and footprints
Executes a comprehensive DNase-seq workflow, processing paired-end FASTQ reads to identify DNase hypersensitive sites (DHSs) and perform transcription factor footprinting. The pipeline leverages Nextflow to manage alignment, peak calling vi…
ENCODE ChIP-seq Processing Pipeline
This Nextflow-based pipeline executes the complete ENCODE ChIP-seq processing workflow, transforming raw FASTQ files into peaks and signal tracks. It handles quality control, alignment, peak calling with MACS2, and IDR analysis using Docker…
ENCODE ATAC-seq Pipeline for Chromatin Accessibility
This tool executes the full ENCODE ATAC-seq workflow, processing raw FASTQ files through alignment, Tn5 offset correction, and rigorous filtering. It generates nucleosome-free peaks and signal tracks following established ENCODE standards.