Usage notes

Pre-sketched databases available for download below. All databases work from sylph version 0.3.x onwards.

Use the Primary links hosted at http://faust.compbio.cs.cmu.edu if possible. We provide mirrors on google cloud, but this costs us more money.

Example usage:

# download database
wget http://faust.compbio.cs.cmu.edu/sylph-stuff/gtdb-r226-c200-dbv1.syldb

# profile against database
sylph profile gtdb-r226-c200-dbv1.syldb -1 sample_R1.fq -2 sample_R2.fq  -t 30 > results.tsv

Note on taxonomy usage:

Most the databases have associated taxonomies that sylph can utilize. See here for more information on taxonomy integration.

Databases

Type	Name	Genomes	c-parameter	Size	Primary Download Link	Mirror	Notes
Prokaryotic (GTDB)	GTDB r226	143,614 species	-c 200	18.4 GB	gtdb-r226-c200-dbv1.syldb	mirror
	GTDB r226	143,614 species	-c 1000	3.7 GB	gtdb-r226-c1000-dbv1.syldb	mirror
	GTDB r220	113,104 species	-c 200	13.1 GB	gtdb-r220-c200-dbv1.syldb	mirror
	GTDB r220	113,104 species	-c 1000	2.6 GB	gtdb-r220-c1000-dbv1.syldb	mirror
	GTDB r214	85,202 species	-c 200	10 GB	v0.3-c200-gtdb-r214.syldb	mirror
	GTDB r214	85,202 species	-c 1000	2 GB	v0.3-c1000-gtdb-r214.syldb	mirror
Prokaryotic (GlobDB)	GlobDB r226	306,260 species	-c 200	32 GB	See the GlobDB website		Third-party database
	GlobDB r226	306,260 species	-c 1000	6.5 GB	See the GlobDB website		Third-party database
Prokaryotic (Other)	OceanDNA	8,466 ocean MAGs	-c 200	800 MB	OceanDNA-c200-v0.3.syldb	mirror
	SMAG	21,077 soil MAGs	200	2.5 GB	SMAG-c200-v0.3.syldb	mirror
	UHGG v2.0.1 (not dereplicated)	289,232 gut genomes	-c 200	26 GB	uhgg_all_c200_v0.3.0.syldb	mirror	Not dereplicated - do not use for profiling
Viral	UHGV	171,338 gut vOTUs	-c 100	0.4 GB	uhgv_c100_dbv1.syldb	mirror
	UHGV	171,338 gut vOTUs	-c 200	0.2 GB	uhgv_c200_dbv1.syldb	mirror
	IMG/VR4.1	2,917,516 viral genomes	-c 200	2 GB	imgvr_c200_v0.3.0.syldb	mirror
Eukaryotic	RefSeq Fungi	595 genomes	-c 200	700 MB	fungi-refseq-2024-07-25-c200-v0.3.syldb	mirror
	TARA Oceans	713 eukaryotic MAGs/SAGs	-c 200	900 MB	tara-eukmags-c200-v0.3.syldb	mirror

Parameter Guide

-c 200: More sensitive, larger file size
-c 1000: More efficient, smaller file size, less sensitive
-c 100: More sensitive but primarily for smaller genomes.

Note

-c 200 is used by default, so -c 100 must be specified if using a database with -c 100. For example:

sylph profile c100_database c1000_database -c100 -1 read1.fq -2 read2.fq.

Database descriptions

GTDB Databases

The GTDB database is a high-quality, curated taxonomy and database for prokaryotes (archaea and bacteria). We take the dereplicated, species-representative genomes (one genome per species).

Available databases:

GTDB r226 database (143,614 species representative genomes) - April 16, 2025
GTDB r220 database (113,104 species representative genomes) - April 24, 2024
GTDB r214 database (85,202 species representative genomes) - April 28, 2023

GlobDB - massive prokaryotic catalogue encompassing many other genome sets

GlobDB is a catalogue of > 300,000 prokaryotic genomes/MAGs. Their database is dereplicated at ~96% ANI. GlobDB encompasses 14 other large databases (including GTDB). The sylph database is hosted on their website.

Other prokaryotic databases

Tip

GlobDB encompasses SMAG and a OceanDNA. We highly recommend using GlobDB if possible over these databases.

OceanDNA catalogue of 8,466 ocean prokaryotic MAGs, -c 200 (800 MB)
SMAG catalogue of soil 21,077 soil MAGs, -c 200 (2.5 GB):
UHGG v2.0.1 catalogue of 289,232 gut genomes. Not dereplicated. Do not use for profiling. -c 200 (26 GB):

Viral databases

Unified Human Gut Virome (UHGV) catalog - (171,338 vOTUs from human gut)
- Note: is more refined and has better taxonomic annotations than IMG/VR for human gut
Pre-sketched IMG/VR4.1 database for high-confidence vOTU representatives (2,917,516 viral genomes).

Eukaryotic databases.

595 representative RefSeq fungi genomes (downloaded 2024-07-25), -c 200 (700 MB)
713 TARA Oceans eukaryotic MAGs/SAGs from Delmont et al., -c 200 (900 MB)