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Install + Quick start

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Very quick start

Profile metagenome against a GTDB database with ~ 200,000 species

Note

See the prebuilt databases for available versions of GTDB.

conda install -c bioconda sylph

# download GTDB pre-built database (~19 GB)
wget http://faust.compbio.cs.cmu.edu/sylph-stuff/gtdb-r232-c200-dbv2.syl2db

# multi-sample paired-end profiling 
sylph profile -d gtdb-r232-c200-dbv2.syl2db -1 *_1.fastq.gz -2 *_2.fastq.gz -t (threads) > profiling.tsv

# multi-sample single-end profiling
sylph profile -d gtdb-r232-c200-dbv2.syl2db -r *.fastq -t (threads) > profiling.tsv

The output file profiling.tsv shows what database genomes are present. This does not have taxonomic information (e.g. species/genus/family). If you want a taxonomic annotations, use sylph-tax.

Install options

Option 1: conda install

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conda install -c bioconda sylph

Option 2: Build from source

Requirements:

  1. rust (version > 1.63) programming language and associated tools such as cargo are required and assumed to be in PATH.
  2. A c compiler (e.g. GCC)
  3. make
  4. cmake

Building takes a few minutes (depending on # of cores).

git clone https://github.com/bluenote-1577/sylph
cd sylph

# If default rust install directory is ~/.cargo
cargo install --path . --root ~/.cargo
sylph profile test_files/*

Option 3: Pre-built x86-64 linux statically compiled executable

If you're on an x86-64 system, you can download the binary and use it without any installation. 

wget https://github.com/bluenote-1577/sylph/releases/download/latest/sylph
chmod +x sylph
./sylph -h

Note: the binary is compiled with a different set of libraries (musl instead of glibc), probably impacting performance.