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.

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

An awesome BCL demultiplexing and FastQ quality-control pipeline

Classification of RNA-Seq samples using circRNA expression

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

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.

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.

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.

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

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

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

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

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

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.