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 Hafnia paralvei Isolate AVS0177, Harboring mcr-9 on a Plasmid

Original Data

• NCBI BioProject: PRJNA761908

• SRA Experiment: SRR15833986

• ENA: SRR15833986

• References (NCBI or Ensembl): Hafnia paralvei

Bioinformatic Analysis

1- Analysis Step​

Application

Long Reads Quality Assessment (LongQC)

Input

• ONT sequencing data in FASTQ format (SRR15833986)

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

• SRR15833986_1_trimmed.fastq: Trimmed reads in FASTQ file