DE NOVO GENOME ASSEMBLY USING LONG READS#

 

Basecalling#

Base calling is the process of translating the electronic raw signal (fast5 format) of the sequencer into bases (fastq format).

• environment: the i-Trop computing cluster.

• software: guppy

• input data: /scratch/genesys_training/files/data/fast5/

• link to the tutorial  

Quality assessment#

Verify the quality of reads within nanopore fastq files.

• environment: the i-Trop computing cluster.

• software: fastqc

• input data: /scratch/genesys_training/files/data/lr_fastq/all_guppy.fastq

• link to the tutorial  

Read filtering, trimming and adapter removal#

Verify the quality of reads within nanopore fastq files.

• environment: the i-Trop computing cluster.

• software: porechop; nanofilt

• input data: /scratch/genesys_training/files/data/lr_fastq/all_guppy.fastq

• link to the tutorial  

Genome assembly#

"De novo" assembly of long reads

• environment: the i-Trop computing cluster.

• software: flye

• input data: Klebsiella pneumoniae nanopore sequences link to input files

• link to the tutorial