quast

A transparent ONT bacterial assembly case study for an *Acinetobacter* barcode07 isolate, built not only to generate an assembly, but to show how raw reads become an interpretable genome through QC evidence, assembler comparison, graph checks, phylogeny, annotation, documented decisions, and honest limitations.

Reusable comparative bacterial genomics pipeline for assembled bacterial genome FASTA files using QUAST, Bakta, FastANI, Panaroo, and FastTree.

Genome assembly quality assessment using QUAST

De novo genome assembly (MaSuRCA), reference-guided scaffolding (RagTag), and QC (QUAST, BUSCO, synteny analysis) for Humulus lupulus cv. Julian Gold

🦇🧫📊Study on bat gut shotgun metagenomics

A modular, reproducible, and automated Bash pipeline for bacterial isolate whole-genome sequencing analysis from Illumina paired-end reads, including quality control, taxonomic classification, genome assembly, genome characterization, and coverage estimation.

End-to-end Pseudomonas carnis WGS pipeline for genome assembly, QC, read mapping, AMR, plasmid & virulence profiling.

A modular Nextflow DSL2 pipeline for reproducible plant de novo genome and transcriptome assembly, quality control, validation, and functional analysis.

Montagem de genoma bacteriano: Trimmomatic, SPAdes, QUAST, Prokka, BLAST

QUAST assembly assessment using a reference genome.

reproducible Snakemake pipeline for bacterial hybrid assembly.

Run multiple metagenome filtering programs using Docker containers

Nanopore genome assembly and quality assessment of Cardamine resedifolia using Flye, QUAST and BUSCO.

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.

[a.a. 24/25] C. Coscarelli, M. Santoriello

Docker container for W2RAP based on CentOS

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

Pipeline bioinformático modular para ensamblaje, evaluación y anotación de genomas bacterianos mediante herramientas reproducibles basadas en Conda.

Automated Bash pipeline for hybrid de novo bacterial genome assembly, combining Oxford Nanopore (ONT) and Illumina reads with QC, polishing (POLCA), and evaluation (QUAST).

E. coli genome assembly and analysis using FastQC, fastp, SPAdes, QUAST and Python.