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

🧹 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.

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.

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

Blazingly fast SRA-scale sequence analysis & QC

A read classification tool based on Interleaved Bloom Filters

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

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

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

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

Python bioinformatics CLI for k-mer counts and de Bruijn graphs

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

🗑️🦷 decOM 🦷🗑️

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

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

Learn interpretable computational phenotyping models from k-merized genomic data

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

SEER, reimplemented in python 🐍🔮

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