Basecalling using Guppy

Base calling is the process of translating the electronic raw signal of the sequencer into bases, i.e., ATCG. As for most bioinformatic tasks there are many different tools to solve this problem. Here, we will only focus on the current state-of-the-art basecaller Guppy, which is the current “official” ONT basecaller. Although basecalling can be performed “live”, i.e., in real time while sequencing, it is often useful to separate the sequencing from basecalling. One advantage of “offline” basecalling is that the basecaller can use significant amounts of compute and read/write resources which may slow the sequencing process and, in rare cases, even lead to loss of sequencing data.

Guppy is a neural network based basecaller that in addition to basecalling also performs filtering of low quality reads, clipping of Oxford Nanopore adapters and estimation of methylation probabilities per base.

Guppy uses significant amounts of compute resources/time if run on a processor (CPU), especially if using the High-Accuracy models. Thus, basecalling especially for larger datasets often requires compute clusters (as provided by the NCI) or specific workstation computers. ONT also released a Guppy version that utilises graphics card chips (GPUs) instead of the “usual” computer processor (CPUs). The GPU version of guppy is significantly faster than the CPU version. However, the installation is restricted to specific computers/graphics cards and can unfortunately not be virtualised, e.g. with VirtualBox.

As input, Guppy, as well as the now deprecated Albacore and all other basecallers, uses files in fast5 format as input.

First, change into the directory /course_data/practicals/basecalling_practical. It contains a sub-directory called fast5 with fast5 files of a recent MinION run.

Apart from the input fast5 files guppy requires a configuration file that sets the basecalling parameters depending on which flowcell and library preparation kit was used to produce the data. To list all supported flowcell and library kits type

guppy_basecaller --print_workflows
Do not copy-paste the commands shown on the tutorial pages! Some characters, e.g., the hyphens, change based on the font used causing random errors in the commands! Even if it seems silly, please type the commands yourself.

The provided data was prepared using the SQK-LSK108 library preparation kit that was sequenced on a MIN106 flowcell.

What’s the name of the configuration file guppy needs to basecall the tutorial data?

Answers

To start the basecalling you can either specify the flowcell and the library kit using the parameters -f FLO-MIN106 and -k SQK-LSK108 or use option –c and the name of the configuration file. For convenience we’ll use the option -c.

guppy_basecaller –i ./fast5 –s ./guppy_out –c dna_r9.4.1_450bps_hac.cfg \
--num_callers 2 --cpu_threads_per_caller 1
The “\” at the end of each line is only for convenience to write a long command into several lines. It tells the command-line that all lines still belong together although they are separated by “enter” keys. However, if you type all of the command, i.e., paths etc, in one line do not copy/type the backslash at the end of the lines.

The command above will call guppy on the input fast5 directory option (-i) and write the output to the directory given with option -s.

The above command will run for several hours! …. therefore please stop Guppy now by pressing Ctrl-c (hold the control key and then press ‘c’) and copy the folder guppy_output from directory course_data/precompiled into the folder basecalling_practical.

Note One of the most common problems/mistakes when copying and moving files arise from incorrect paths. Keep in mind

To copy a directory use the following command

cp –R SOURCE_TO_COPY DESTINATION

where

Change into the directory guppy_output and have a look what is in there. As you can see there are several .fastq files with the basecalled reads, one or more .log files that contains log messages from guppy as well as a sequencing_summary.txt file.

It is often useful to concatenate all the different fastq files into one big file for downstream analyses. From within the guppy_output directory use the cat command to do this:

cat *.fastq > all_guppy.fastq

This will create one fastq file called all_guppy.fastq with all your basecalled reads in it.