In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

SEER, reimplemented in python 🐍🔮

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

Remove contaminated contigs from genomes using k-mers and taxonomies.

Learn interpretable computational phenotyping models from k-merized genomic data

An RNA virus strain-level identification tool for short reads.

Detect complete horizontal gene transfer (HGT) event rapidly and accurately from complex metagenomics data.

Python CLI for alignment-free genomics.

🧹🦷 aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets

This repository contains the results and comparison visualization of circRNA candidates detected by circRNA prediction softwares.

🗑️🦷 decOM 🦷🗑️

Computational programs and algorithms used to convert information from biochemical experiments (DNA/RNA/Protein/DNA chip/NGS) into useful information and data.

🧹 aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets

A Python bioinformatics tool for genomic pseudo-alignment, variant calling (SNPs), and coverage analysis.

A read classification tool based on Interleaved Bloom Filters

simple desktop app that apply some of DNA searching algorithms, with easy use desktop GUI using Pyqt6 lib in python.

Mutation table of COVID-19 virus genome with all possible substitution mutations and corresponding 20-mers for mutation identification

A simple python script that counts k-mer matches between reference database and query .fasta files, optionally returning all non-matching query sequences. Designed originally for sequencing adapter decontamination.

K-mer search enabled fast bacterial DNA sequence retrieval with DNA sequence analysis of Pittsburgh rivers.