unassigner 1.0.0

Description:

unassigner 1.0.0

Unassigner







Evaluate consistency with named bacterial species for short 16S rRNA
marker gene sequences.
Summary
The 16S rRNA gene
is 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 in
microbiome
research. 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 the Streptococcus genus 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 for ruling out assignment 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 the unassigner. 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.
Installation
Install with conda using:
conda create --name unassigner -c conda-forge -c bioconda unassigner

Or run with Docker using:
docker run --rm -it ctbushman/unassigner:latest unassign --help

Alternative Installation
Unassigner can be installed using pip:
pip install unassigner

But will require vsearch to be installed separately. It can also be installed from GitHub:
git clone https://github.com/PennChopMicrobiomeProgram/unassigner.git
pip install unassigner/

Usage
The unassign program requires one argument, a FASTA-formatted file
of short 16S sequences:
unassign my_sequences.fasta

If 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 named my_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 as my_sequences.fasta.
Please see the output of unassign --help for a list of the available
options.
Contributing
We 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.