Package: unassigner
UnassignerEvaluate consistency with named bacterial species for short 16S rRNA
marker gene sequences.SummaryThe16S rRNA geneis found in all bacteria, and its gene sequence is highly
conserved. Amplification and sequencing of bacterial 16S rRNA genes is
a common method used to survey bacterial communities inmicrobiomeresearch. However, high throughput instruments are unable to sequence
the entire gene. Therefore, a short region of the gene is selected for
amplification and sequencing.The resultant sequences, spanning part of the 16S gene, can be used to
identify the types of bacteria present in a specimen. For example, one
sequence might be assigned to theStreptococcusgenus based on
sequence similarity. Many programs are available to carry out such
taxonomic assignment.It is generally thought that the 16S rRNA gene is not suitable for
assignment of bacterial species. We agree, but with a catch: the gene
sequence is suitable forruling outassignment to many bacterial
species. This software is designed to rule out all the species
designations that are inconsistent with a partial 16S rRNA gene
sequence. For those species that are not definitively ruled out, we
assign a probability that the sequence is inconsistent with the
species.Because the software is geared towards ruling out species rather than
deciding on the best assignment, we call it theunassigner. It's a
cheesy joke, but we've decided to roll with it.The unassigner library provides a command-line program,unassign,
that takes a FASTA file of DNA sequences in a 16S gene region, and
gives the probability that the sequence is inconsistent with nearby
bacterial species.InstallationThe Python library and command-line program can be installed usingpip.pipinstallunassignerBesides the python libraries listed in the setup file, this program
requiresvsearchto be installed.  This program is used to search
for the closest matching bacterial species and return pairwise
sequence alignments.  It's available throughconda, and this is our
recommended method for installation.condacreate--nameunassigner
condaactivateunassigner
condainstall-cbiocondavsearch
pipinstallunassignerAlternative InstallationIfpip install unassignerisn't working or if you want to use a development
version, you can also install via git.condacreate--nameunassigner
condaactivateunassigner
condainstall-cbiocondavsearch
gitclonehttps://github.com/kylebittinger/unassigner.gitcdunassigner
pipinstall-rrequirements.txt
pipinstall.If you don't want to use conda, see thevsearch repofor alternative install
methods.UsageTheunassignprogram requires one argument, a FASTA-formatted file
of short 16S sequences:unassignmy_sequences.fastaIf the program has not been run before, it will automatically download
the bacterial species data it needs, format its reference files,
create an output directory namedmy_sequences_unassigned, and write
a table of results there, along with some auxiliary output files. Note
that the output directory will be in the same directory asmy_sequences.fasta.Please see the output ofunassign --helpfor a list of the available
options.ContributingWe welcome ideas from our users about how to improve this
software. Please open an issue if you have a question or would like to
suggest a feature.