This is a CRISPR-Cas mining pipeline designed for UNIX and Linux operating systems. The pipeline accepts a nucleotide FASTA file (https://en.wikipedia.org/wiki/FASTA_format). Currently, the pipeline is being built for individual bacterial or archaeal genomes, but will later be usable with metagenomic read data.
This pipeline is written in Python and utilizes SCons for reproducible builds and analyses. #--------------------------------- Prerequisites #--------------------------------- Install these dependencies first: Python 3: pandas ggpy (not yet implemented) Biopython SCons 3.0.1 Prodigal 2.x or higher HMMER 3.1 or higher MinCED PilerCR MUSCLE MAFFT #----------------------------------- Usage #----------------------------------- The components of the pipeline include Database and Pipeline builds.
The Database build will construct profile Hidden Markov Models (HMMs) from single multiple sequence alignments (MSA) or several corresponding MSAs.
The Pipeline build mines the FASTA file for Cas genes and CRISPR arrays, finds clusters, and updates profile HMMs with newly discovered proteins.
The SConstruct files control the builds: pipeline/SConstruct database/SConstruct
To run, use: scons --fasta=<file.fna>
#----------------------------------- Authors #----------------------------------- Ian Rambo - The University of Texas at Austin Marine Science Institute
#----------------------------------- Acknowledgements #----------------------------------- https://www.scons.org/ https://github.com/ctSkennerton/minced http://eddylab.org/software/hmmer/hmmer.org https://www.drive5.com/muscle/ https://www.drive5.com/pilercr/ https://github.com/hyattpd/Prodigal http://scons.org/