| name | singlem |
| description | SingleM — species-level metagenome profiling from conserved windows in universal marker genes, including lineages without genomic representation; Sandpiper aggregates public SingleM profiles. Use when: (1) Profiling environmental communities rich in unknowns, (2) Feeding Bin Chicken coassembly targeting, (3) GTDB-linked marker OTUs from short reads, (4) Comparing to MetaPhlAn/mOTUs/sylph. Upstream: https://github.com/wwood/singlem. Sandpiper: https://sandpiper.qut.edu.au.
|
| license | MIT |
| category | analysis-tools |
| tags | ["SingleM","taxonomy","markers","Sandpiper","low-abundance"] |
| upstream | https://github.com/wwood/singlem |
| stage | taxonomy |
SingleM (+ Sandpiper)
Upstream: wwood/singlem ·
Sandpiper: https://sandpiper.qut.edu.au
Citation
Woodcroft, B. J. et al. Comprehensive taxonomic identification of microbial
species in metagenomic data using SingleM and Sandpiper. Nat. Biotechnol.
(2025). https://doi.org/10.1038/s41587-025-02738-1
See also docs/references.md.
Analytical thinking
Most profilers under-count species without reference genomes. SingleM
recruits reads covering short conserved windows in universal markers (AA-aware
via DIAMOND), clusters 60-bp windows into OTUs, then assigns taxonomy with
GTDB-oriented alignment (smafa). Unknown species can dominate environmental
communities in SingleM/Sandpiper analyses — state that as a profiling result,
not as MAG recovery.
| Tool | Role |
|---|
singlem | Profile your metagenomes (incl. novel lineages) |
binchicken | Uses SingleM-style marker sharing to plan coassemblies |
metaphlan / motus | Marker packs / SCGs — complementary, different unknown handling |
| Sandpiper | Browse 248k+ public SingleM profiles |
How to run
singlem pipe -1 clean_1.fq.gz -2 clean_2.fq.gz -o temp/singlem/${id} --threads 16
Pin SingleM metapackage / GTDB-linked DB version in Methods.
Decision tree
Taxonomic profiling need?
├─ Environment with many unknowns → singlem
├─ Targeted coassembly of rare lineages → singlem → binchicken
├─ Named SGB marker packs / pathways → metaphlan (± humann)
├─ Sketch containment vs genomes → sylph
└─ MAG taxonomy → gtdbtk
Related skills
binchicken · metaphlan · motus · sylph · gtdb · study-design ·
tool-selection
