CroCoDeEL detects cross-sample contamination in shotgun metagenomic data
☆32Sep 8, 2026Updated last month
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-…☆43Updated this week
- A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.☆56Sep 28, 2026Updated 2 weeks ago
- gemsparcl 💎✨ Rapid and consistent clustering of millions of genomes highlights the diversity of prokaryotic life☆19Jun 16, 2026Updated 3 months ago
- ☆10Jun 9, 2025Updated last year
- A repo to reproduce the experiments in the YACHT manuscript☆12Nov 2, 2023Updated 2 years ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- ☆33Oct 1, 2026Updated last week
- Modeling strain-level variation by gene, phylogeny, or pathway☆14Aug 6, 2026Updated 2 months ago
- ☆16Jun 2, 2021Updated 5 years ago
- TAXnomic Profile Aggregation and STAndardisation☆43May 2, 2026Updated 5 months ago
- Repository for codes, analyses and visualizations for the CAMI II challenges☆15Sep 4, 2023Updated 3 years ago
- 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 2 years ago
- PanTax: Strain-level metagenomic profiling using pangenome graphs☆54Jun 10, 2026Updated 4 months ago
- ☆12Jun 3, 2025Updated last year
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- ☆21Sep 16, 2026Updated 3 weeks ago
- Resolving Species Level Classification Using Emu☆14Jun 14, 2024Updated 2 years ago
- Visualize microbial evolution at the SNP level!☆18Aug 12, 2025Updated last year
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆64Sep 1, 2026Updated last month
- AMR/VF LGT focused bacterial genomics analysis workflow☆28Feb 19, 2026Updated 7 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆71Apr 10, 2025Updated last year
- MaAsLin3: Microbiome Multivariate Association with Linear Models☆87Sep 15, 2026Updated 3 weeks ago
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆49Jun 19, 2026Updated 3 months ago
- ☆85Aug 23, 2026Updated last month
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- From dereplication to genome enrichment: Enhancing genome recovery across metagenomic samples using MAGmax☆37Aug 28, 2026Updated last month
- Build a partitioned pangenome graph from microbial genomes☆312Oct 6, 2026Updated last week
- Fast pairwise transmission inference from single genome and/or metagenomic data☆39Aug 21, 2026Updated last month
- Workflow for MAG quality assessment and taxonomical annotation.☆15May 26, 2026Updated 4 months ago
- A functional profiler for metagenomes using FracMinHash☆22Apr 20, 2026Updated 5 months ago
- ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.☆325Updated this week
- Amplicon sequencing variants from modern nanopore / HiFi long read amplicons☆65Oct 8, 2026Updated last week
- Public repository for cFMD - curatedFoodMetagenomicData☆39Jun 18, 2026Updated 3 months ago
- Clustering tool optimized for sparse distance matrices: ~16M elements with ~190M connections clustered in minutes.☆16Sep 12, 2026Updated last month
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Fast, accurate taxonomic assignments for the human vaginal microbiota☆11Mar 19, 2026Updated 6 months ago
- SourceTracker2☆92Jul 10, 2024Updated 2 years ago
- Development repo for pyani-plus (the next iteration of pyani)☆36Oct 6, 2026Updated last week
- Bin Chicken - recovery of low abundance and taxonomically targeted metagenome assembled genomes (MAGs) through strategic coassembly☆78Oct 7, 2026Updated last week
- Metaphor: a general-purpose workflow for assembly and binning of metagenomes☆40Nov 14, 2025Updated 11 months ago
- snakemake-powered cli to download genomes using NCBI datasets☆15Aug 14, 2025Updated last year
- Precise host read removal☆132Apr 13, 2026Updated 6 months ago