caltha 0.4

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: 12)

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)

• 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
• McKinney W,
  Data Structures for Statistical Computing in Python.
  Proceedings of the 9th Python in Science Conference. 2010.
  Pandas

Author(s)

• Jasper Boom

Citation

• Boom J, Caltha. 2019.
  
  GitHub repository: https://github.com/JasperBoom/caltha