Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes
☆183Mar 19, 2026Updated this week
Alternatives and similar repositories for singlem
Users that are interested in singlem are comparing it to the libraries listed below
Sorting:
- A hybrid assembly and MAG recovery pipeline (and more!)☆104Jan 27, 2026Updated last month
- Read alignment statistics for metagenomics☆392Updated this week
- ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.☆298Feb 3, 2026Updated last month
- Bin Chicken - recovery of low abundance and taxonomically targeted metagenome assembled genomes (MAGs) through strategic coassembly☆72Mar 3, 2026Updated 2 weeks ago
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆240Oct 12, 2025Updated 5 months ago
- Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!☆179Updated this week
- More scalable dereplication for metagenome assembled genomes☆78Mar 8, 2026Updated last week
- Bioinformatics program inStrain☆182Mar 12, 2026Updated last week
- Rapid comparison and dereplication of genomes☆329Nov 10, 2025Updated 4 months ago
- Assessing the quality of metagenome-derived genome bins using machine learning☆252Mar 20, 2025Updated last year
- Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes☆323Updated this week
- Variational autoencoder for metagenomic binning☆319Feb 23, 2026Updated 3 weeks ago
- Assessing and Improving the quality of metagenomic assemblies☆31Feb 21, 2022Updated 4 years ago
- A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during…☆82Sep 8, 2025Updated 6 months ago
- Python package for detection of chimerism and contamination in prokaryotic genomes.☆82Mar 12, 2026Updated last week
- A scalable high-throughput metabolic and biogeochemical functional trait profiler☆219Jan 27, 2025Updated last year
- SemiBin: metagenomics binning with self-supervised deep learning☆156Feb 19, 2026Updated last month
- 🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes☆81Dec 4, 2025Updated 3 months ago
- GraftM - Rapid community profiles from metagenomes☆50Nov 6, 2025Updated 4 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
- MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.☆212Mar 3, 2026Updated 2 weeks ago
- ☆25Jun 20, 2023Updated 2 years ago
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆612Feb 18, 2026Updated last month
- geNomad: Identification of mobile genetic elements☆296Updated this week
- Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.☆170Jan 2, 2026Updated 2 months ago
- Reorients assembled microbial sequences☆136Aug 21, 2025Updated 7 months ago
- Phage annotations and predictions. A spae is a prediction or foretelling. We'll foretell you what your phage is doing!☆41Feb 26, 2026Updated 3 weeks ago
- PanTax: Strain-level metagenomic profiling using pangenome graphs☆49Mar 2, 2026Updated 2 weeks ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆54Sep 7, 2025Updated 6 months ago
- alignment-free coverage calculation for metagenomic binning >100 times faster☆50Mar 13, 2025Updated last year
- GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.☆585Feb 21, 2026Updated last month
- A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.☆45Feb 5, 2026Updated last month
- Accurate metagenomic profiling && Fast large-scale sequence/genome searching☆208Sep 22, 2023Updated 2 years ago
- ☆81Mar 13, 2026Updated last week
- Taxonomy classification of viral sequences / contigs☆12Jul 15, 2025Updated 8 months ago
- Remove human reads from a sequencing run☆48Mar 9, 2026Updated last week
- Binning Virus Genomes from Metagenomes☆72Jul 13, 2022Updated 3 years ago
- Scalable creating/updating of metagenome profiling databases☆62Jun 25, 2025Updated 8 months ago
- CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metage…☆227Jan 20, 2026Updated 2 months ago