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).

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

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.

An awesome BCL demultiplexing and FastQ quality-control pipeline

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

A reproducible Whole Genome Sequencing (WGS) quality-control pipeline for Bacterial Genomics using FastQC, MultiQC, and fastp.

Classification of RNA-Seq samples using circRNA expression

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

Single-sample Nextflow DSL2 workflow for FASTQ preprocessing, reference alignment, BAM processing, and alignment QC.

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

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

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

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

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.

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

NGS quality control and preprocessing using fastp and FastQC in Ubuntu WSL

Modular Bash pipeline from an SRA accession to a gene-level count matrix: fastp trimming, HISAT2 alignment, featureCounts quantification, with per-stage QC.