Table 1 Bioinformatics tools that use minimizers categorized in seven fields, namely, read alignment, read correction, de Bruijn graph (dBG) representation, genome assembly, pangenomes, metagenomics classification, and assembly

Read alignment

minimap2

Uses a seed-chain-align procedure by collecting minimizers

[40, 41]

GraphAligner

Long-read aligner to genome graphs using minimizers

[42]

LRA

Aligns long reads to a reference genome

[43]

Chromap

Aligns chromatin profiles using minimizers

[44]

Winnowmap and Winnowmap2

Weighted-minimizer sampling algorithm that builds on top of minimap2

[45, 46]

Read correction

Miniscrub

Convolutional neural network-based method for removing low-quality nanopore read segments

[47]

VeChat

Correcting errors in long reads using variation graphs

[48]

isONcorrect

Long-read error correction

[49]

Minirmd

Removing duplicate and near-duplicate reads

[50]

de Bruijn graph (dBG) representation

BCALM2

Parallel dBG compaction

[51]

Bifrost

Parallel dBG compaction

[52]

GGCAT

Parallel k-mer enumeration and dBG compaction

[53]

Fulgor

ccdBG representation for alignment-free sequence matching

[54]

De novo genome assembly

rust-mdBG

De novo genome assembly from minimizer-space dBG

[55]

MBG

De novo genome assembly from minimizer-based dBG

[55, 56]

LJA

Long-reads de novo genome assembly

[57]

ntJoin

Reference-based genome assembly

[58]

Wengan

Hybrid short- and long-reads de novo genome assembly

[59]

Pangenomes

Minigraph

Pangenome construction from multiple genomes (Eukaryote-vertebrate focus) and sequence to graph aligner

[60]

Giraffe

Fast mapping of short-reads to pangenome (Eukaryote-vertebrate focus)

[61]

PGR-TK

Pangenome construction and analysis using sparse hierarchical minimizers (Human focus)

[62]

Pandora

Pangenome construction and analysis. Capture core and accessory genes as well as variants (Bacteria focus)

[63]

Metagenomics classification

Kraken and Kraken2

Metagenomics classifier by minimizer with improved memory requirements

[64, 65]

K2Mem

Classifier based on kraken2 with improved memory and classification time

[66]

MetaMaps

Analyzer for long-read metagenomics data

[67]

Metagenomics assembly

MetaProb2

Genome binning method using minimizers to assemble reads

[68]