Nanopore Assembly Workflow

Quality Control

Nanopore does it's own QC for the reads. Ignore the failed reads. fast5 format has additional information about the sequenced reads but you can use fastq for this step.

The "sequencing summary" file has information about each sequence and also has mean qscore: quality score

#Concatenate all your "pass" reads into one giant fastq file
cat ./fastq_pass/*.fastq.gz > all_passed_reads.fastq.gz

The Guppy basecaller does quality control and demultiplexing for us. This is extra.

Porechop 0.2.41 with default settings can be used for adapter trimming. Can be used on barcoded reads for demultiplexing (separating based on barcodes) and adapter trimming. Porechop is no longer supported but there isn't anything else to do this job. There's several deficiencies with Porechop (read on Github)

For filtering reads above a length or quality, use Nanofilt

#to download, I used conda
conda create -n porechop
conda activate porechop
conda install -c bioconda porechop

#for porechop help
porechop -h

#to run porechop
porechop -i all_passed_reads.fastq.gz -o all_passed_reads_trimmed.fastq.gz -t 12