Welcome to the Nucleotide sequence analysis took kit, a set of command line utilities for managing larger volumes of nucleotide sequences all based in the R-programming language. These utilities take advantange of BioConductoR packages, including Biostrings, ShortRead, and GenomicRanges.
For documentation on the utilities, please refer to ReadTheDocs.io.
For quick installation, follow the commands below on the command line of a linux OS:
git clone https://github.com/cnobles/nuckit.git
cd nuckit
bash install.sh -b
An overview of the utilities included can be found using the [-h] flag:
conda activate nuckit
nuckit -h
usage: nuckit [-h/--help, -v/--version] <subcommand>
NucKit - Nucleotide sequence analysis took kit!
subcommands:
demulti Demultiplex Illumina sequence files given various barcoding schemes.
trim Trim leading and/or over-reading sequences from sequence files.
filt Filter sequences in one or more sequence files by various criteria.
consol Consolidate reads to unique sequences and generate a key file.
couple Couple independent BLAT alignments from paired-end sequences.
optional arguments:
--nuckit_dir NUCKIT_DIR
Path to NucKit installation. (default:/home/nobles/nuckit)
-v, --version show program's version number and exit
For more help, see the docs at http://nuckit.readthedocs.io.