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.
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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 pip or conda. This dependency is VSEARCH (2.14.1+).
Conda can be used to easily install this 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] [-p DISIDENTITY] [-c DISABUNDANCE]
[-w DISFORWARD] [-r DISREVERSE] [-d FISDIRECTORY]
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.
-t FOSTABULAR, -tabular FOSTABULAR
The location of the output tabular file.
-z FOSPREZIP, -zip FOSPREZIP
The location of the pre validation zip file.
-b FOSBLAST, -blast FOSBLAST
The location of the output fasta file.
-f DISFORMAT, -format DISFORMAT
The format of the input file [fasta/fastq].
-s DISSEARCH, -search DISSEARCH
Search UMIs at the 5'-end [umi5], 3'-end [umi3] or at
the 5'-end and 3'-end [umidouble].
-a DISAPPROACH, -approach DISAPPROACH
The UMI search approach [primer/adapter/zero].
-u DISUMILENGTH, -length DISUMILENGTH
The length of the UMI sequence.
-p DISIDENTITY, -identity DISIDENTITY
The identity percentage with which to perform the
validation.
-c DISABUNDANCE, -abundance DISABUNDANCE
The minimum abundance of a read in order to be
included during validation.
-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.
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)
- 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
Author(s)
Citation
- Boom J, Caltha. 2019.
GitHub repository: https://github.com/JasperBoom/caltha
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