========= DeeNuRP

16S rRNA gene sequence curation and phylogenetic reference set creation

Installation

The Easy Way

• confirm availability of necessary libraries to compile dependencies (on Ubuntu: sudo apt-get install gfortran libopenblas-dev liblapack-dev)

• Install Python >= 3.8 or Python 3 Virtual Environment ::

  % python3 -m venv bin-env % source bin-env/bin/activate % bin/bootstrap.sh

the deenurp executable should now be on your $PATH

The Hard Way

See required system libraries above.

First, install binary dependencies:

• Python 3

  • pip, for installing python dependencies (http://www.pip-installer.org/)

  • Python packages:

    • Run pip install PACKAGE for every PACKAGE listed in requirements.txt, e.g. cat requirements.txt | xargs -n 1 pip install

• vsearch (https://github.com/torognes/vsearch)

• Infernal version 1.1 (http://infernal.janelia.org/)

• pplacer suite (http://matsen.fhcrc.org/pplacer)

• FastTree 2 (http://www.microbesonline.org/fasttree/#Install)

Optional (for filter-outliers and pairwise-distances):

• muscle (http://www.drive5.com/muscle/)

Finally, install::

python setup.py install

The Docker Way

Deenurp can be run from a Docker image which can be built locally from the Dockerfile or pulled docker pull nghoffman/deenurp:v0.3.0

De-novo reference set creation

Similarity-search based reference sequence selection

Running

The deenurp package under the current directory provides to subcommands, accessed via the script deenurp.py, or the command deenurp if installed.

Subcommands fall into two general categories:

• Building a set of reference sequences for use in refpkg building
• Selecting sequences for a specific reference package

Creating a sequence set for refpkg building

deenurp filter-outliers

Removes outlier sequences from a reference database

``deenurp expand-named``

Expands poorly-represented names in a sequence file by similarity search

deenurp cluster-refs

Cluster reference sequences, first by tax-id at a specified rank
(default: species), then by similarity for unnamed sequences or
sequences not classified to the desired rank.  Serves as input to
``search-sequences``.

Selecting sequences for a reference package
-------------------------------------------

``deenurp hrefpkg-build``

Builds a set of hierarchical reference packages.

deenurp search-sequences

Searches a set of sequences against a FASTA file containing possible
reference sequences.

This subcommand does searches sequences against a reference FASTA
file, saving the results and some metadata to a sqlite database for
use in ``select-references``

``deenurp select-references``

Given the output of search-sequences, select-references attempts to find a good set of reference sequences.

For each reference cluster with a minimal amount of sequences having best hits to the cluster, (see cluster-refs), selects a set number of sequences to serve as references.

deenurp fill-lonely

Taxa who are the sole descendent of their parent can complicate
taxonomic classification.

The ``fill-lonely`` subcommand finds some company for these lonely
taxa.

``deenurp add-reps``

Fetches sequences from a sequence file which match the taxtable for a reference set at a given rank. Useful for adding type strains.

deenurp tax2tree

Runs the ``tax2tree`` program on a reference package, updating the
``seq_info`` file.

Sequences whose lineage changes are relabeled. The prior ``tax_id`` is
added to the ``seq_info`` file in the reference package.