Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline

An awesome BCL demultiplexing and FastQ quality-control pipeline

Nextflow pipeline for separating host and viral reads and identifying viral mutations from sequencing data.

Pipeline para análise de dados genómicos com FastQC, MultiQC e FastP. Inclui scripts para preparação de ambiente, análise de qualidade e execução interativa para verificação de comandos no Conda.

Classification of RNA-Seq samples using circRNA expression

This project uses an workflow pipeline to generate map and assemble RNAseq reads to a reference genome. Furthermore, we generate counts data and identify differentially expressed genes from 2 conditions.

Low-compute Nextflow pipeline for single-cell RNAseq QC using pseudo-alignment. Two-mode design: with laptop-friendly quick mode for QC and cost prediction, HPC/cloud full mode for Cell Ranger comparable results. Validated on Element AVITI and Illumina NextSeq 2000 sequencing data using 10X V3 Chromium chemistry. Outputs feed scanpy/Seurat directly

Reusable bacterial genome analysis pipeline for paired-end FASTQ data using FastQC, fastp, SPAdes, QUAST, Prokka, and MultiQC.

Hands-on implementation of a SARS-CoV-2 variant calling pipeline using NGS data and Linux-based bioinformatics tools.

Nextflow-based pipeline for the end-to-end analysis of ChIP-seq datasets

The repository contains a comprehensive pipeline for genome assembly and quality assessment, designed for genomic data analysis. It integrates various bioinformatics tools for accurate genome assembly.