CroCoDeEL is a tool that detects cross-sample contamination in shotgun metagenomic data
☆27Apr 13, 2026Updated this week
Alternatives and similar repositories for CroCoDeEL
Users that are interested in CroCoDeEL are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Meteor is a plateform for quantitative metagenomics profiling of complex ecosystems. Meteor relies on genes catalogue to perform species-…☆37Apr 7, 2026Updated last week
- A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.☆49Feb 5, 2026Updated 2 months ago
- ☆10Jun 9, 2025Updated 10 months ago
- A repo to reproduce the experiments in the YACHT manuscript☆11Nov 2, 2023Updated 2 years ago
- ☆32Jan 4, 2025Updated last year
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- ☆13Jul 21, 2025Updated 8 months ago
- TAXnomic Profile Aggregation and STAndardisation☆42Nov 18, 2025Updated 4 months ago
- Repository for codes, analyses and visualizations for the CAMI II challenges☆14Sep 4, 2023Updated 2 years ago
- ☆15Jun 2, 2021Updated 4 years ago
- Development repo for pyani-plus (the next iteration of pyani)☆30Apr 7, 2026Updated last week
- Calculate confidence scores from Kraken2 output☆25Feb 18, 2024Updated 2 years ago
- Code used to analyse and plot metadata of metagenomic binning tools☆14Aug 22, 2024Updated last year
- A command-line tool for profiling CAZyme abundances in metagenomic datasets.☆17Updated this week
- ☆11Jun 3, 2025Updated 10 months ago
- Wordpress hosting with auto-scaling - Free Trial • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Rapidly extract reads from a FASTQ file based on taxonomic classification via Kraken2.☆13Jan 26, 2026Updated 2 months ago
- ☆20Apr 7, 2026Updated last week
- Resolving Species Level Classification Using Emu☆14Jun 14, 2024Updated last year
- Visualize microbial evolution at the SNP level!☆15Aug 12, 2025Updated 8 months ago
- Public repository for cFMD - curatedFoodMetagenomicData☆33Feb 12, 2026Updated 2 months ago
- AMR/VF LGT focused bacterial genomics analysis workflow☆28Feb 19, 2026Updated last month
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated last year
- ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.☆301Feb 3, 2026Updated 2 months ago
- ☆72Mar 10, 2024Updated 2 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆47Apr 1, 2025Updated last year
- Build a partitioned pangenome graph from microbial genomes☆297Mar 30, 2026Updated 2 weeks ago
- Basecalling configuration prediction through FASTQ files☆33Mar 17, 2026Updated 3 weeks ago
- The binning tool with dynamic contrastive learning and deep language model☆22Nov 14, 2025Updated 5 months ago
- From dereplication to genome enrichment: Enhancing genome recovery across metagenomic samples using MAGmax☆27Updated this week
- Precise host read removal☆119Mar 28, 2026Updated 2 weeks ago
- Snakemake pipeline for simulating shotgun metagenomic samples☆29Mar 13, 2026Updated last month
- snakemake-powered cli to download genomes using NCBI datasets☆15Aug 14, 2025Updated 8 months ago
- Software to trim the ITS region of FASTQ sequences for amplicon sequencing analysis☆17Mar 26, 2025Updated last year
- Wordpress hosting with auto-scaling - Free Trial • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Fast, accurate taxonomic assignments for the human vaginal microbiota☆11Mar 19, 2026Updated 3 weeks ago
- SourceTracker2☆86Jul 10, 2024Updated last year
- A functional profiler for metagenomes using FracMinHash☆21Apr 3, 2026Updated last week
- Assessing the quality of metagenome-derived genome bins using machine learning☆252Mar 20, 2025Updated last year
- Metaphor: a general-purpose workflow for assembly and binning of metagenomes☆40Nov 14, 2025Updated 5 months ago
- strain-level analysis tools☆39Oct 21, 2024Updated last year
- MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data☆399Mar 16, 2026Updated last month