snpDensityMatrix is a tool used to analize SNP pipeline output and build graphical output for SNP density, read depth, and PHI statistic. It is designed to detect probable homologous recombination events, which are often characterized as regions of abnormally high SNP density.
- Python: Version 3.4 or greater.
- SAMTools: Version 1.4.1 or greater.
- VCFTools: Version 0.1.15 or greater.
snpDensityMatrix primarily runs by calling the snpDensityMatrix.py script and can be cloned basically anywhere without the need to compile anything. All of the accompanying HTML, CSS, and JavaScript files are a barebones offline web application that will be copied to the working directory upon use and therefore must be kept in their current locations after cloning the repo.
The following is a strict step by step guide that must be followed in the proper order:
- Clone this repo to the directory of your choosing.
- Add this directory to your path.
- Done.
snpDensityMatrix is called with the following command line prompt:
$ snpDensityMatrix.py [-h, --help] [--window WINDOW] [--step STEP] [--nasp | --cfsan | --lyve | --snvphyl] DIR
[-h, --help]- Displays the help menu for snpDensityMatrix before exiting.
[--window WINDOW]- Optional argument with a default value of 10000. Set size of capture window to measure snp density.
[--step STEP]- Optional argument with a default value of 5000. Set step size to move window down snp matrix.
[--nasp | --cfsan | --lyve | --snvphyl]- Required argument must be chosen and must match the intended snp pipeline format. Flag used for snp pipeline format.
DIR- Required Positional argument. Root directory for snp pipeline output.
Running snpDensityMatrix to get the snp density visualization for snp pipeline output located at './example/snpOut/', with a window size of 1000 and a step size of 500:
$ /installDirectory/snpDensityMatrix.py --window 1000 --step 500 --nasp ./example/snpOut/
Would result in the command line output:
====================( Job Starting: snpDensityMatrix.py )
(1/4) gathering coverage from BAM/VCF files
creating file "./snpDensityOut/snpPositions.txt"
creating file "./snpDensityOut/Sample1-Depth.txt" (1 of 4)
creating file "./snpDensityOut/Sample2-Depth.txt" (2 of 4)
creating file "./snpDensityOut/Sample3-Depth.txt" (3 of 4)
creating file "./snpDensityOut/Sample4-Depth.txt" (4 of 4)
waiting for threads to return ▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉
(2/4) writing export and excise data files
creating EXCISE file ...
creating EXPORT file ▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉
(3/4) processing hash table
processing 1 of 1 contigs ▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉
processing 2 of 2 contigs ▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉
(4/4) writing results csv file
creating file "./snpDensityOut/snpDensityMatrix.csv"
====================( Total Time: 0:0:0:30 )
====================( Job Complete: snpDensityMatrix.py )
nonHomologous is a separate script for detecting non-homologous recombination. It also operates on SNP Pipeline output, but looks at the accessory genomes of all the samples in your dataset.
- Python: Version 3.4 or greater.
- MUMmer: Version 3.0 or greater.
- SPAdes: Version 3.10 or greater.
- SAMTools: Version 1.4.1 or greater.
- bedtools: Version 2.18 or greater.
- SLURM: Any version is probably okay. This is currently a requirement in order to efficiently assemble all of the accessory genomes from your data set. Other job managers could be supported easily enough, but we are hesitant to do this without a job manager, as there may be thousands of samples in your data set.
nonHomologous primarily runs by calling the nonHomologous.sh script and can be cloned basically anywhere without the need to compile anything. Two other scripts that are part of this repo, assembleUmappedReads (bash) and alignAccessoryGenomes (python3) NEED to be in your path, as well as each of the required prerequisite programs.
The following is a strict step by step guide that must be followed in the proper order:
- Clone this repo to the directory of your choosing.
- Add this directory to your path.
- Done.
nonHomologous is called with the following command line prompt:
$ nonHomologous.py [-h] -b BAMDIR -o OUTDIR
[-h]- Displays the help menu for nonHomologous before exiting.
-b BAMDIR- Required argument pointing to a directory of bam files (probably output by your chosen SNP pipeline) that are to be analyzed.
-o OUTDIR- Required argument giving a directory where output files are to be written. It will be created if it doesn't already exist.
This pipeline will perform the following steps:
- Find all bam files in the supplied directory and extract the unmapped reads from each
- Assemble the unmapped reads into contigs
- Concatenate all the contigs together into a single file (
accessory_genomes_combined.fasta) - Dispose of all contigs that don't meet the length (5000bp) and coverage (2x) thresholds (
accessory_genomes_trimmed.fasta) - Align these contigs to themselves, ignoring any alignments within the same original sample
- Display all pairwise alignments longer than 5000bp (
pairwise_aligned.out)