kmer

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.

Generate unique KMERs for every contig in a FASTA file

Classify sequencing reads using MinHash.

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

Ultra-rapid detection of viral variants directly from sequencing data

Fast and space-efficient taxonomic classification of long reads

Predict plasmids from uncorrected long read data

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

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

k-mer similarity analysis pipeline

Count kmers with a more efficient (faster) hash table

Topsicle utilizes abundance of telomere pattern k-mers to estimate telomere length in long read.

Ultrafast sequence typing and gene detection from NGS raw reads