A python package to process UMI tagged mixed amplicon metabarcoding data.
Project description
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
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)
Citation
- Boom J, Caltha.
GitHub repository: https://github.com/JasperBoom/caltha
Copyright (C) 2018 Jasper Boom (jboom@infernum.nl)
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/>.
Project details
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
caltha-0.5.1.tar.gz
(9.6 kB
view hashes)
Built Distribution
caltha-0.5.1-py3-none-any.whl
(22.3 kB
view hashes)