DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

Quickly search, compare, and analyze genomic and metagenomic data sets.

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Accurate metagenomic profiling && Fast large-scale sequence/genome searching

De novo genome assembly and multisample variant calling

modular k-mer count matrix and Bloom filter construction for large read collections

A versatile toolkit for k-mers with taxonomic information

To phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.

Classify sequencing reads using MinHash.

Fast and space-efficient taxonomic classification of long reads

Generate unique KMERs for every contig in a FASTA file

Fast k-mer based tool for multi locus sequence typing (MLST)

Predict plasmids from uncorrected long read data

Bioinformatics 101 tool for counting unique k-length substrings in DNA

Count kmers with a more efficient (faster) hash table

Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.

Ultrafast sequence typing and gene detection from NGS raw reads

k-mer similarity analysis pipeline

fast and comprehensive k-mer counting package

🎯 Generate DNA sequences with specified amino acid, codon, and k-mer frequencies