---
title: "Long Reads Quality Assessment"
canonical: "https://help.biobam.com/space/OBD/3050176513/Long%20Reads%20Quality%20Assessment"
format: markdown
---
# Introduction

Nanopore long read sequencing of *Hafnia paralvei* AVS0177

### Dataset description

Oxford Nanopore sequencing reads from *Hafnia paralvei* strain:AVS0177

- Genomic DNA seq
- MinION device on a FLO-MIN106 flow cell (Oxford Nanopore Technologies)

### Publication

[Complete Genome Sequence of ](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8759386/)*[Hafnia paralvei](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8759386/)*[ Isolate AVS0177, Harboring mcr-9 on a Plasmid](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8759386/) 

### Original Data

- NCBI BioProject: [PRJNA761908](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA761908)
- SRA Experiment: [SRR15833986](https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR15833986)
- ENA: [SRR15833986](https://www.ebi.ac.uk/ena/browser/view/SRR15833986?show=reads)
- References (NCBI or Ensembl): *[Hafnia paralvei](https://www.ncbi.nlm.nih.gov/genome/15874?genome_assembly_id=1703148)*

# Bioinformatic Analysis

## 1- Analysis Step​

### Application

[Long Reads Quality Assessment (LongQC)](https://biobam.atlassian.net/wiki/spaces/~772013725/pages/3029205008) 

### Input

- [ONT sequencing data in FASTQ format (SRR15833986)](https://drive.google.com/file/d/1c24xmAMCQmDT8y9jDWBUbe2VRl8QUQKq/view?usp=sharing)

### Parameters

- Sequencing Technology: Nanopore (Ligation Sequencing Kit)
- Transcript mode: false
- Short mode: false
- Save trimmed reads: true

### Execution Time

5-10 min

### Output

- [SRR15833986.box: Results object from LongQC](https://drive.google.com/file/d/1teXL5C3E6vggu4aFueSPGpkCSN3_uR3B/view?usp=sharing)
- [SRR15833986_1_trimmed.fastq: Trimmed reads in FASTQ file](https://drive.google.com/file/d/1jO6DMB_4sTSN0oxL5yvyXwh5udq26En3/view?usp=sharing)