A python package for processing UMI tagged mixed amplicon metabarcoding data.
The current version of Caltha requires Python 3.8.
To install Caltha, simply run the pip install command:
pip install caltha
NOTE: Caltha does require one more dependency which can not be installed
with the Caltha PyPI package. This dependency is
vsearch (2.15.0).
Conda can be used to manage
the installation of this tool.
After installation of either anaconda or miniconda, executing the following
conda install command should install the dependency.
conda install -c bioconda vsearch=2.15.2
Caltha can be run directly from the command line.
usage: caltha [-h] [-v] [-i FLINPUT] [-t FLTABULAR] [-z FLPREVALIDATION]
[-b FLBLAST] [-f [{fasta,fastq}]] [-l [{umi5,umi3,umidouble}]]
[-a [{primer,adapter,zero}]] [-u INTUMILENGTH] [-y FLTIDENTITY]
[-c INTABUNDANCE] [-w STRFORWARD] [-r STRREVERSE]
[-d STRDIRECTORY] [-@ INTTHREADS]
A python package for processing 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 FLINPUT, --input FLINPUT
The input fasta/fastq file(s). This can either be a
zip archive or a single fasta/fastq file.
-t FLTABULAR, --tabular FLTABULAR
The output tabular zip file.
-z FLPREVALIDATION, --zip FLPREVALIDATION
The pre validation zip file.
-b FLBLAST, --blast FLBLAST
The output blast zip file.
-f [{fasta,fastq}], --format [{fasta,fastq}]
The format of the input file. (default: fasta)
-l [{umi5,umi3,umidouble}], --location [{umi5,umi3,umidouble}]
Search for UMIs at the 5'-end, 3'-end or at the 5'-end
and 3'-end. (default: umi5)
-a [{primer,adapter,zero}], --anchor [{primer,adapter,zero}]
Which anchor type to use. (default: primer)
-u INTUMILENGTH, --length INTUMILENGTH
The length of the UMI sequence. (default: 5)
-y FLTIDENTITY, --identity FLTIDENTITY
The identity percentage with which to perform
the validation. (default: 0.97)
-c INTABUNDANCE, --abundance INTABUNDANCE
The minimum abundance of a sequence in order for
it to be included during validation. (default: 1)
-w STRFORWARD, --forward STRFORWARD
The 5'-end anchor nucleotides.
-r STRREVERSE, --reverse STRREVERSE
The 3'-end anchor nucleotides.
-d STRDIRECTORY, --directory STRDIRECTORY
The location of the temporary working
directory (not created by Caltha). (default: .)
-@ INTTHREADS, --threads INTTHREADS
The number of threads to run Caltha with. (default: 8)
This python package requires one extra dependency which can be easily
installed with conda (conda install -c bioconda vsearch=2.15.0).
Further documentation can be found here.
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GitHub repository: https://github.com/JasperBoom/caltha
Copyright (C) 2018 Jasper Boom
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/>.