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.

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

An awesome BCL demultiplexing and FastQ quality-control pipeline

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

Interactive FastQC-style quality control and read trimming for FASTQ files: drag to trim, see the exact fastp command, compare before and after. Windows (TrimView.exe), macOS, Linux.

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

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.

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

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

Germline variant calling pipeline (bwa, samtools, bcftools, SnpEff) for targeted cancer panel data from the public SEQC2 reference sample, with an R/Quarto report.

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

End-to-end RNA-seq differential expression pipeline (fastq-dump → fastp → Salmon → PyDESeq2) analyzing dexamethasone treatment effects in airway smooth muscle cells, with PCA, volcano plots, and pathway enrichment analysis.

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