PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)
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Updated
Jul 3, 2024 - Python
PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)
SEER, reimplemented in python 🐍🔮
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.
🧹🦷 aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
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
simple desktop app that apply some of DNA searching algorithms, with easy use desktop GUI using Pyqt6 lib in python.
🗑️🦷 decOM 🦷🗑️
Remove contaminated contigs from genomes using k-mers and taxonomies.
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.
🧹 aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets
Learn interpretable computational phenotyping models from k-merized genomic data
This repository contains the results and comparison visualization of circRNA candidates detected by circRNA prediction softwares.
Mutation table of COVID-19 virus genome with all possible substitution mutations and corresponding 20-mers for mutation identification
A read classification tool based on Interleaved Bloom Filters
Computational programs and algorithms used to convert information from biochemical experiments (DNA/RNA/Protein/DNA chip/NGS) into useful information and data.
K-mer search enabled fast bacterial DNA sequence retrieval with DNA sequence analysis of Pittsburgh rivers.
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