Table 2.

Main long-read bioinformatics tools for targeted and shotgun approaches.

Type	Reference	Application	Brief description
Aligners/Alignment-based classifiers
BLAST, MEGABLAST	[58], [59]	Targeted; Shotgun	Gold-standard alignment tools for classification of nucleotide and protein sequences. Feature web-based version and multiple implementations for specific purposes.
minimap2	[33]	Targeted; Shotgun	Versatile tool for fast read alignments against large reference databases.
Alignment-free classifiers
Kraken, Kraken2	[35], [64]	Targeted; Shotgun	Taxonomic classification tool implementing an accurate and fast k-mer matching.
KrakenUniq	[65]	Shotgun	Classifier that combines Kraken classification tool with the assessment of the coverage of unique k-mers for better recall and precision.
Bracken	[66]	Targeted; Shotgun	Relative abundance estimation tool for single-level abundance using Kraken read classification output.
Metamaps	[69]	Shotgun	Read assignment and sample composition estimation for nanopore metagenomic datasets.
Centrifuge	[34]	Targeted; Shotgun	Read classification based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index that performs fast classification relying on small pre-computed index databases.
Mash	[72]	Targeted; Shotgun	Fast genome and metagenome distance estimation tool that computes distances between sequences using the MinHash algorithm.
Long-read assemblers
Canu	[90]	Shotgun	Assembly pipeline for long-reads that compute and process read overlaps for the generation of contigs and draft assemblies.
miniasm	[73]	Shotgun	Fast OLC-based assembler for long reads that builds assembly graphs from all-vs-all read mappings.
wtdbg2	[91]	Shotgun	De-novo sequence assembler for uncorrected long-reads based on Fuzzy Bruijn graphs to compute contigs.
OPERA-MS	[95]	Shotgun	Hybrid metagenomic assembler that first performs a short-read assembly and then maps short and long reads to resolve contiguity of contigs.
MetaFlye	[96]	Shotgun	Metagenomic assembler from the Flye package featuring repeat graphs to compute high-quality metagenome assemblies.
MetaSPAdes	[74]	Shotgun	Metagenomic assembly module from SPAdes assembler that features a hybrid assembly option.
Sequence correction and polishing tools
Nanopolish	https://github.com/jts/nanopolish	Targeted; Shotgun	Signal-level analysis tool with modules that performs sequence polishing, base modification detection and variant calling.
Medaka	https://github.com/nanoporetech/medaka	Targeted; Shotgun	Neural network-based sequence correction and variant calling tool.
Metagenomic analysis pipelines
MEGAN-LR	[60]	Shotgun	Long-read implementation of the MEGAN workflow. Features taxonomic and functional analysis.
NanoCLUST	[25]	Targeted	Analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads.
Reticulatus	https://github.com/SamStudio8/reticulatus	Shotgun	Snakemake-based pipeline for assembly and polishing of long genomes from long nanopore reads.
MUFFIN	[70]	Shotgun	Metagenomics workflow for hybrid assembly, differential coverage binning, transcriptomics and pathway analysis.
NanoSPC	[71]	Shotgun	Metagenomic analysis pipeline that includes viral and bacterial pathogen identification, genome assembly and variant calling.
BusyBee	https://ccb-microbe.cs.uni-saarland.de/busybee/	Shotgun	Web-based metagenomic analysis pipeline for long-reads and contigs that features taxonomic and functional annotation of AMR elements along with a comprehensive visualization of results.