sipost1 / kraken2OTUtableView external linksLinks
Creates a simple OTU table from Kraken2 report.
☆13Oct 15, 2024Updated last year
Alternatives and similar repositories for kraken2OTUtable
Users that are interested in kraken2OTUtable are comparing it to the libraries listed below
Sorting:
- Calculate confidence scores from Kraken2 output☆23Feb 18, 2024Updated last year
- A Rust-based library for phylogenetic analysis and manipulation☆16Updated this week
- Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on…☆12May 22, 2024Updated last year
- Development repo for pyani-plus (the next iteration of pyani)☆24Jan 26, 2026Updated 2 weeks ago
- Needleman-Wunsch Alignment in Go☆12Nov 9, 2020Updated 5 years ago
- ☆16Apr 6, 2023Updated 2 years ago
- Computation of average nucleotide identity with the use of MMseqs2☆15Dec 11, 2024Updated last year
- A "Navie" Implementation of the Wavefront Algorithm For Sequence Alignment with Gap-Affine Scoring☆14Aug 7, 2023Updated 2 years ago
- Rust implementation of the XXH3 hash function☆27Aug 10, 2025Updated 6 months ago
- Fast and Memory Efficient Genome Sketching via HyperLogLog, HyperMinHash and UltraLogLog☆19Jan 22, 2026Updated 3 weeks ago
- This repository houses the code to run SURPI+, a rapid computational pipeline for comprehensive identification of pathogens from clinical…☆42Nov 20, 2019Updated 6 years ago
- Minimum plain text representation of kmer sets☆16Jan 30, 2025Updated last year
- Kraken2 Server☆23Nov 24, 2025Updated 2 months ago
- Taxonomic classifier for sequencing reads (bulk and single-cell data, short and long read) using FM-index with run-block compressed BWT.☆84Feb 7, 2026Updated last week
- MetagenOmic read Re-Assigner and abundance quantifier☆20Jan 31, 2025Updated last year
- create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks☆57Dec 12, 2025Updated 2 months ago
- RabbitMash: an efficient highly optimized implementation of Mash.☆20Oct 28, 2023Updated 2 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆63Apr 10, 2025Updated 10 months ago
- Compute a pairwise SNP distance matrix from one or two alignment(s)☆26Sep 12, 2024Updated last year
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆24Feb 6, 2023Updated 3 years ago
- Catalogue of pairwise alignment algorithms and benchmarks☆25Jan 6, 2026Updated last month
- Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…☆57Feb 7, 2026Updated last week
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆29Aug 20, 2025Updated 5 months ago
- k-Medoids clustering in Rust with the FasterPAM algorithm☆27Sep 17, 2025Updated 4 months ago
- A sanity checker for global allocations in Rust☆52Sep 11, 2025Updated 5 months ago
- Reference-quality genome reconstruction from complex metagenomes (or bacterial isolates) using only Nanopore long reads or both long and …☆33Oct 17, 2023Updated 2 years ago
- Efficient and fast querying and parsing of GTDB's data☆29Aug 21, 2025Updated 5 months ago
- LRBinner is a long-read binning tool published in WABI 2021 proceedings and AMB.☆32May 30, 2023Updated 2 years ago
- Dashing 2 is a fast toolkit for k-mer and minimizer encoding, sketching, comparison, and indexing.☆70Jun 17, 2024Updated last year
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆65Jun 16, 2025Updated 7 months ago
- A novel method for sequence similarity estimation☆28Mar 23, 2024Updated last year
- A genome diagram generator for microbes and organelles☆57Updated this week
- A method of assessing sequence complexity based on kmer frequencies☆33Apr 9, 2018Updated 7 years ago
- A SIMD-accelerated library to compute random minimizers☆36Jan 20, 2026Updated 3 weeks ago
- Kmer Analysis of Pileups for Genotyping☆35Jan 30, 2026Updated 2 weeks ago
- Workshop: Using R/tidyverse to analyze & visualize gapminder/processed transcriptomics data!☆13Sep 12, 2025Updated 5 months ago
- Fast, Cache-Efficient, and Scalable Queries on Pangenomes☆36Nov 7, 2025Updated 3 months ago
- MD5 hash cracking with CUDA and Rust, implemented from scratch☆46Dec 31, 2024Updated last year
- PLSDB pipeline to collect bacterial plasmids from NCBI☆39Oct 23, 2024Updated last year