Install + Quick start

Install

Install option 1 - Conda

conda install -c bioconda sylph-tax

Install option 2 - Python

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

Quick start

Step 1: Profile using one or more of the available databases with sylph

# profile something with pre-built GTDB_r220 / IMGVR_4.1 databases
sylph profile .... gtdb-r220-c200-dbv1.syldb imgvr_c200_v0.3.0.syldb  > sylph_results/my_result.tsv

Step 2: use sylph-tax to get taxonomic profile

• Download the taxonomy files (only needs to be done once)

# download all taxonomy files (~50 MB)
sylph-tax download --download-to /any/folder

• Use sylph-tax taxprof and specify the sylph-tax identifiers in this table (the first column) corresponding to your database

# incorporate GTDB-r220 and IMGVR-4.1 taxonomies into sylph's results
sylph-tax taxprof sylph_results/*.tsv -t GTDB_r220 IMGVR_4.1 -o output_prefix-

ls output_prefix-sample1.sylphmpa
ls output_prefix-sample2.sylphmpa
...

• Merge results (optional)

# merge multiple results
sylph-tax merge *.sylphmpa --column relative_abundance -o merged_abundance_file.tsv