caltha 0.5.1

A python package to process UMI tagged mixed amplicon metabarcoding data.

Caltha

A python package to process UMI tagged mixed amplicon metabarcoding data.

Installation

The current version of Caltha requires Python 3.7+.

To install Caltha, simply run the pip install command or the conda install command:

pip install caltha

conda install -c jboom caltha

NOTE: Caltha does require one more dependency which can not be installed with the Caltha pip or conda package. This dependency is Vsearch (2.14.1+).
Executing the following conda install command should install the dependency.

conda install -c bioconda vsearch

How to run

Caltha can be run directly from the command line.

caltha -h

usage: caltha [-h] [-v] [-i FISINPUT] [-t FOSTABULAR] [-z FOSPREZIP]
              [-b FOSBLAST] [-f DISFORMAT] [-s DISSEARCH] [-a DISAPPROACH]
              [-u DISUMILENGTH] [-y DISIDENTITY] [-c DISABUNDANCE]
              [-w DISFORWARD] [-r DISREVERSE] [-d FISDIRECTORY]
              [-p DISPROCESSES]

A python package to process UMI tagged mixed amplicon metabarcoding data.

optional arguments:
  -h, --help            show this help message and exit
  -v, -version          show program's version number and exit
  -i FISINPUT, -input FISINPUT
                        The location of the input fasta/fastq file(s).
  -t FOSTABULAR, -tabular FOSTABULAR
                        The location of the output tabular zip file.
  -z FOSPREZIP, -zip FOSPREZIP
                        The location of the pre validation zip file.
  -b FOSBLAST, -blast FOSBLAST
                        The location of the output blast zip file.
  -f DISFORMAT, -format DISFORMAT
                        The format of the input file
                        [fasta/fastq/zipfasta/zipfastq].
  -s DISSEARCH, -search DISSEARCH
                        Search UMIs at the 5'-end [umi5], 3'-end [umi3] or at
                        the 5'-end and 3'-end [umidouble]. (default: umi5)
  -a DISAPPROACH, -approach DISAPPROACH
                        The UMI search approach [primer/adapter/zero].
                        (default: primer)
  -u DISUMILENGTH, -length DISUMILENGTH
                        The length of the UMI sequence.
  -y DISIDENTITY, -identity DISIDENTITY
                        The identity percentage with which to perform the
                        validation. (default: 0.97)
  -c DISABUNDANCE, -abundance DISABUNDANCE
                        The minimum abundance of a read in order to be
                        included during validation. (default: 1)
  -w DISFORWARD, -forward DISFORWARD
                        The 5'-end search nucleotides.
  -r DISREVERSE, -reverse DISREVERSE
                        The 3'-end search nucleotides.
  -d FISDIRECTORY, -directory FISDIRECTORY
                        The location where the temporary working directory
                        will be created. (default: .)
  -p DISPROCESSES, -processes DISPROCESSES
                        The number of threads/cores/processes to
                        simultaneously run Caltha with. (default: number of cores available)

This python package requires one extra dependency which can be easily
installed with conda (conda install -c bioconda vsearch).

Further documentation can be found here.

Package links

• PyPI
• Conda

Source(s)

• Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P,
  Galaxy: A platform for interactive large-scale genome analysis.
  Genome Research. 2005; 15(10) 1451-1455. doi: 10.1101/gr.4086505
  Galaxy
• Python Software Foundation,
  Python 3.7+. 2019.
  Python
• Rognes T, Flouri T, Nichols B, Quince C, Mahe F,
  VSEARCH: A versatile open source tool for metagenomics.
  PeerJ. 2016. doi: 10.7717/peerj.2584
  Vsearch
• Augspurger T, Ayd W, Bartak C, Battiston P, Cloud P, Garcia M,
  Python Data Analysis Library.
  Pandas
• Langa L, Willing C, Meyer C, Zijlstra J, Naylor M, Dollenstein Z,
  The uncompromising Python code formatter.
  Black

Author(s)

• Jasper Boom

Citation

• Boom J, Caltha.
  GitHub repository: https://github.com/JasperBoom/caltha

Copyright (C) 2018 Jasper Boom ([e-mail])

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License version 3 as 
published by the Free Software Foundation.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.