FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )
Creates a simple OTU table from Kraken2 report.
A post-processing tool to reclassify Kraken 2 output based on the confidence score and/or minimum minimizer hit groups.
2024"猛犸杯"参赛作品 · 宏基因组学端到端分析流程
🗂️Parse multiple Kraken2 reports into CSV files on 6 taxonomical levels
a simple python script for "grafting" on novel sequences to a custom Kraken2 database
Unified short-read workflow for multi-marker amplicon (16S, ITS, 18S, gyrB, rpoB) and shotgun taxonomic profiling. Snakemake, conda-based, reproducible.
Quantifies microbial composition from host-aligned sequencing data.
An awesome BCL demultiplexing and FastQ quality-control pipeline
Script to extract species abundance from Kraken2 report file
Kanatlı mikrobiyom Nanopore metagenomik analiz pipeline'ı — Nextflow DSL2 + Docker + Kraken2
#Scripts to create Kraken2 database of PAFTOL V2.0 Angio353 genes. An excellent database for taxonomic identification of plants. #https://treeoflife.kew.org/ #https://github.com/DerrickWood/kraken2/wiki #Prior to using this script, download and install kraken2 and make sure it is working and in your PATH. #Make sure the location of the python sc…
Containerized Snakemake workflow that diagnoses why short-read samples align poorly — contamination, vector/transgene, rRNA, adapter, and spike-in multimapping — and identifies the unaligned reads in a self-contained HTML report.
Snakemake workflow for ONT adaptive sequencing data integrating QC, taxonomy (Kraken2), rejected read analysis, and control vs adaptive comparison.
Three-headed host removal for metagenomic data: assembly, profiling and privacy-scrubbed outputs from one run.
Reproducible Snakemake workflow for ONT metagenomic microbiome analysis with multi-tool taxonomic assignment, consensus comparison, and diversity analysis.
SweetBITS: a suite of sweet command-line tools for Kraken 2 derived data and the Swedish Biodiversity in Time and Space (SweBITS) project.
A reproducible QIIME 2 MOSHPIT pipeline that assembles, bins, dereplicates and taxonomically classifies whole‑metagenome data. Includes MEGAHIT assembly, MetaBAT 2 binning, BUSCO quality control, Sourmash dereplication and Kraken 2/Bracken abundance estimation. Ideal for microbial‑ecology, functional‑genomics and strain‑level profiling studies.
Reproducible Snakemake workflow for building reference databases (Kraken2, CAT, BLAST) for metagenomic analysis.
Add a description, image, and links to the kraken2 topic page so that developers can more easily learn about it.
To associate your repository with the kraken2 topic, visit your repo's landing page and select "manage topics."