fastp

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

Assembly of Nanopore Sequencing

A complete bioinformatics pipeline (FastQC, fastp, HISAT2, featureCounts, DESeq2) for RNA-Seq DGE analysis of Klebsiella pneumoniae (WT vs. ΔcpxR).

End-to-end DNA sequencing variant calling and functional annotation pipeline using FastQC, fastp, BWA-MEM, SAMtools, Picard, GATK HaplotypeCaller, and Ensembl VEP on human NGS datasets.

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

An awesome BCL demultiplexing and FastQ quality-control pipeline

Reproducible quality control and preprocessing for paired-end RNA-seq FASTQ files

Tumor-normal variant analysis workflow using Nextflow DSL2, FastQC, Fastp, BWA, GATK, ANNOVAR and IGV visualization.

NGS Quality Control Pipeline using FastQC, Fastp, and MultiQC for Illumina paired-end sequencing data.

Automated NGS pipeline for Mycobacterium leprae antimicrobial resistance prediction using BWA, SAMtools, BCFtools and snpEff

A reproducible RNA-seq analysis pipeline built with Nextflow and Docker, supporting QC, alignment, quantification, differential expression, transcript discovery, and automated reporting.

Classification of RNA-Seq samples using circRNA expression

Modular and reproducible Illumina RNA-seq pipeline built with Nextflow DSL2 and Docker.

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.

A reproducible Linux-based RNA-seq preprocessing workflow including quality control, trimming, alignment, BAM processing, and gene-level quantification.

A bioinformatic workflow for quality control, read trimming ,read statistics and metagenome assembly using FastQC, fastp, Seqkit and MEGAHIT

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

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.