Inspect the output

The directory contains the following output:

ls -l ~/workdir/data_artic/basecall_tiny

total 4544
-rw-rw-r-- 1 ubuntu ubuntu 2356539 Nov  4 10:03 fastq_runid_ca07d29b288c9f8881387334d8fc7d195fb11339_0_0.fastq.gz
-rw-rw-r-- 1 ubuntu ubuntu 1209378 Nov  4 10:03 guppy_basecaller_log-2020-11-04_09-54-21.log
-rw-rw-r-- 1 ubuntu ubuntu  969796 Nov  4 10:03 sequencing_summary.txt
-rw-rw-r-- 1 ubuntu ubuntu  108243 Nov  4 10:03 sequencing_telemetry.js

So we have one fastq file in our directory - since we started with one fast5 file. Ususally, we should merge all resulting fastq files into a single file:

cat ~/workdir/data_artic/basecall_tiny/*.fastq.gz > ~/workdir/data_artic/basecall_tiny.fastq.gz

In order to get the number of reads in our fastq file, we can count the number of lines and divide by 4:

zcat ~/workdir/data_artic/basecall_tiny.fastq.gz | wc -l | awk '{print $1/4}'

And to get the number of bases:

zcat ~/workdir/data_artic/basecall_tiny.fastq.gz | paste - - - - | cut -f 2 | tr -d '\n' | wc -c

With a genome size of ~30k we get a coverage of:

zcat ~/workdir/data_artic/basecall_tiny.fastq.gz | paste - - - - | cut -f 2 | tr -d '\n' | wc -c | awk '{print $1/30000}'