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Install + Quick start

Very quick start

Profile metagenome sample against GTDB-R220 (113,104 bacterial/archaeal species)

conda install -c bioconda sylph

# download GTDB-R220 pre-built database (~13 GB)
wget http://faust.compbio.cs.cmu.edu/sylph-stuff/gtdb-r220-c200-dbv1.syldb

# multi-sample paired-end profiling (sylph version >= 0.6)
sylph profile gtdb-r220-c200-dbv1.syldb -1 *_1.fastq.gz -2 *_2.fastq.gz -t (threads) > profiling.tsv

# multi-sample single-end profiling
sylph profile gtdb-r220-c200-dbv1.syldb *.fastq -t (threads) > profiling.tsv

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.