CroCoDeEL is a tool that detects cross-sample contamination in shotgun metagenomic data
☆28Feb 20, 2026Updated 2 weeks ago
Alternatives and similar repositories for CroCoDeEL
Users that are interested in CroCoDeEL are comparing it to the libraries listed below
Sorting:
- Meteor is a plateform for quantitative metagenomics profiling of complex ecosystems. Meteor relies on genes catalogue to perform species-…☆37Feb 17, 2026Updated 2 weeks ago
- A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.☆44Feb 5, 2026Updated last month
- Rapidly extract reads from a FASTQ file based on taxonomic classification via Kraken2.☆13Jan 26, 2026Updated last month
- ☆10Jun 9, 2025Updated 8 months ago
- A repo to reproduce the experiments in the YACHT manuscript☆11Nov 2, 2023Updated 2 years ago
- Development repo for pyani-plus (the next iteration of pyani)☆25Feb 25, 2026Updated last week
- Visualize microbial evolution at the SNP level!☆15Aug 12, 2025Updated 6 months ago
- ☆15Jun 2, 2021Updated 4 years ago
- ☆11Jun 3, 2025Updated 9 months ago
- Resolving Species Level Classification Using Emu☆14Jun 14, 2024Updated last year
- Calculate confidence scores from Kraken2 output☆24Feb 18, 2024Updated 2 years ago
- TAXnomic Profile Aggregation and STAndardisation☆42Nov 18, 2025Updated 3 months ago
- Repository for codes, analyses and visualizations for the CAMI II challenges☆14Sep 4, 2023Updated 2 years ago
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated last year
- Code used to analyse and plot metadata of metagenomic binning tools☆14Aug 22, 2024Updated last year
- The binning tool with dynamic contrastive learning and deep language model☆21Nov 14, 2025Updated 3 months ago
- ☆32Jan 4, 2025Updated last year
- Basecalling configuration prediction through FASTQ files☆33Nov 24, 2025Updated 3 months ago
- Fast, accurate taxonomic assignments for the human vaginal microbiota☆11Feb 11, 2026Updated 3 weeks ago
- A functional profiler for metagenomes using FracMinHash☆21Jul 14, 2025Updated 7 months ago
- A streamlined workflow and GUI for real-time species identification and pathogen characterization via nanopore sequencing data. Engineere…☆20Oct 4, 2024Updated last year
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆47Feb 20, 2026Updated 2 weeks ago
- ☆69Mar 10, 2024Updated last year
- ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.☆297Feb 3, 2026Updated last month
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴 𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆47Apr 1, 2025Updated 11 months ago
- Deepurify is a tool to filter the contaminated contigs in a MAG with a language model.☆23Jun 3, 2025Updated 9 months ago
- BRICK creates a BRIG-like interactive data visualisation for bacterial genome annotations and comparisons☆21Dec 9, 2025Updated 2 months ago
- Metaphor: a general-purpose workflow for assembly and binning of metagenomes☆40Nov 14, 2025Updated 3 months ago
- Precise host read removal☆117Sep 4, 2025Updated 6 months ago
- MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs☆25Mar 19, 2023Updated 2 years ago
- ☆11Mar 10, 2024Updated last year
- A command-line tool for profiling CAZyme abundances in metagenomic datasets.☆15Feb 27, 2026Updated last week
- ☆11Jul 21, 2025Updated 7 months ago
- 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
- AMR/VF LGT focused bacterial genomics analysis workflow☆28Feb 19, 2026Updated 2 weeks ago
- Snakemake pipeline for simulating shotgun metagenomic samples☆29Sep 4, 2025Updated 6 months ago
- Public repository for cFMD - curatedFoodMetagenomicData☆33Feb 12, 2026Updated 3 weeks ago
- SourceTracker2☆86Jul 10, 2024Updated last year
- Open-source usearch☆132Aug 19, 2025Updated 6 months ago