Meteor

Build instructions

First, you will need cargo. To install it, we recommend using rustup, which can be installed easily as follows (this includes cargo):

curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- --profile minimal --default-toolchain nightly

Note: You may need some basic packages. These include, at least, curl and gcc/clang.

Then you can restart your terminal and install meteor as follows (by default, it is installed in ~/.cargo/bin):

cargo +nightly install --git https://github.com/biocom-uib/meteor

This can take a while to build, but it is completely automatic.

Usage

Meteor has four main subcommands, which are usually run the same order as explained. To obtain more information on each command, use meteor <subcommand> --help.

fetch

This utility subcommand can automatically download related files to be used by Meteor. For instance, you can download the NCBI Taxonomy as follows

meteor fetch ncbi-taxonomy -d download/ncbi-taxonomy

preprocess-taxonomy

This subcommand loads, preprocesses and serializes the provided taxonomy (i.e. NCBI's). To use the NCBI taxonomy, download and extract it (it can be found here). Assuming that the extracted taxonomy is in download/ncbi-taxonomy, you could run

meteor preprocess-taxonomy download/ncbi-taxonomy taxonomy.bin --contract

Note that this step only needs to be run once per taxonomy update.

get-lineage

This subcommand can be used to obtain the lineage from a list (one per line) of taxids from the preprocessed taxonomy. Example:

meteor get-lineage --taxonomy taxonomy.bin <<< $'1\n2'

preprocess-blastout

This subcommand loads the output of NCBI's BLAST+ (blastn) to produce a suitable input file for the tango-assign subcommand. Assuming that blastn was executed using -outfmt '6 qseqid staxid' or -outfmt '7 qseqid staxid' and, for instance, -db nt:

meteor preprocess-blastout /path/to/blast/hits.out \
    --blast-outfmt '7 qseqid staxid' \
    --query-id-col qseqid \
    --subject-id-col staxid \
    --output preprocessed_hits.tsv

The argument to --blast-outfmt should be exactly the same as blastn's -outfmt, but only supports formats 6 and 7. Columns staxid and ssciname are not included by default but at least one of those is required by tango-assign (staxid is preferred), see blastn -help for more information about specifying output columns).

tango-assign

This subcommand assigns hits from preprocess-blastout to nodes in the taxonomy. This is a reimplementation of TANGO using the serialized taxonomy from the preprocess-taxonomy step and the output from preprocess-blastout. To run it, execute

meteor tango-assign taxonomy.bin preprocessed_hits.tsv -q 0.5 -o assignment.tsv

crispr-match

This optional step uses MinCED to find CRISPR spacers in the metagenomic sample and BLAST to match them with viral contigs. Assuming that MinCED is downloaded as minced.jar and BLAST installed in $PATH, the sample command would be

meteor crispr-match /path/to/viral/contigs.fa /path/to/metagenomic/seqs.fa \
    --minced minced.jar --output crispr-matches.tsv

refine-vpf-class

This step takes as input the results from tango-assign and the host prediction output from vpf-class (GitHub) and refines it to include only ascendants from taxonomic nodes found in the tango-assign step. If the output is located at /path/to/vpf-class/output/, then the refinement of the host_genus prediction can be done as follows:

meteor refine-vpf-class taxonomy.bin assignment.tsv \
    /path/to/vpf-class/output/host_genus.tsv \
    -o refined_host_genus.tsv

The output contains two additional columns: for each VPF-Class prediction, assigned_taxids is a semicolon-separated list of taxids found in assignment.tsv which are descendants of this prediction and assigned_contigs is a semicolon-separated list of the metagenomic contigs that were grouped as those descendants.

To include data from crispr-match (and keep only host predictions with matching CRISPR spacers), use the flag --crispr-matches to specify the path to crispr-matches.tsv. This includes additional columns related to CRISPR matches.

Uninstallation

Simply remove ~/.cargo/bin/meteor. If you wish to uninstall rustup too, run

rustup self uninstall