Important
Documentation for sylph has moved to https://sylph-docs.github.io/. All GitHub documentation (e.g., Wikis) are out of date.
Sylph is a tool for ultrafast taxonomic profiling of metagenomic shotgun reads. Sylph can detect species and their abundances against massive databases such as GTDB (~200k genomes) in seconds.
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Ultrafast, multithreaded, multi-sample: sylph can be > 50x faster than other methods. Sylph only takes ~5 GB of RAM for profiling against the entire GTDB-R232 database (200k genomes).
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Precise species-level profiling: sylph has less false positives than Kraken and is about as precise and sensitive as marker gene methods (MetaPhlAn, mOTUs).
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Accurate (containment) ANI information: sylph can give accurate ANI estimates between reference genomes and your metagenome sample down to 0.1x coverage.
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Customizable databases and pre-built databases: We offer pre-built databases of prokaryotes, viruses, eukaryotes. Custom databases (e.g. using your own MAGs) are easy to build.
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Short or long reads: Sylph works for nanopore, PacBio, and short reads. Sylph is the most accurate method on Oxford Nanopore's independent benchmarks.
Documentation, installation, and usage information is available at https://sylph-docs.github.io/.
Jim Shaw and Yun William Yu. Rapid species-level metagenome profiling and containment estimation with sylph (2024). Nature Biotechnology.