Core Pipelines – Simoes-Costa Lab

This repository contains core analysis scripts and computational utilities used in the Simoes-Costa Lab for the processing and analysis of next-generation sequencing (NGS) data.

The goal of this repository is to provide transparent, easy-to-understand scripts that can be used and adapted by lab members for common genomics workflows.

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Available Pipelines

The repository currently provides scripts supporting the following workflows:

• RNA-seq alignment and processing pipelines using:
  • HISAT2
  • STAR
• ATAC-seq alignment and processing pipelines including peak calling.
• CUT&RUN alignment and processing pipelines including peak calling.

Both paired-end and single-end configurations are supported for RNA-seq.

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Usage

1. Edit the configuration section at the top of the relevant script.
2. Specify genome references and FASTQ inputs.
3. Run the script from the command line.

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Requirements

These workflows assume a Linux environment with common bioinformatics tools installed.

Some dependencies include:

• fastqc
• bowtie2
• HISAT2
• STAR
• samtools
• macs2
• featureCounts

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Maintainer

Computational organization and infrastructure currently maintained by:

Helena B. Conceição
Postdoctoral Researcher – Computational Genomics