LYVE version of the Snp Extraction Tool (SET), a method of using hqSNPs to create a phylogeny. Lyve-SET is meant to be run on a cluster but will just run system calls if qsub is not present.
NML, part of PHAC, has the original version of SET (https://github.com/apetkau). However, I have been updating it since inception and so the results might differ slightly.
make installmake help- for othermakeoptions- See INSTALL.md for more information including prerequisite software
Here is a way to just try out the test dataset.
set_test.pl lambda --numcpus 8 # or however many cpus you want
set_test.pl listeria_monocytogenes --numcpus 8 # or another dataset
Make Lyve-SET go quickly with --fast! This option is shorthand for several other options that save on computational time. See launch_set.pl usage below for more details.
set_test.pl listeria_monocytogenes --numcpus 8 --fast
See: examples.md for more details.
Also see: testdata.md for more details on making your own test data set.
To see the help for any script, run it without options or with --help. For example, set_test.pl -h. The following is the help for the main script, launch_set.pl:
Usage: launch_set.pl [project] [-ref reference.fasta|reference.gbk]
If project is not given, then it is assumed to be the current working directory.
If reference is not given, then it is assumed to be proj/reference/reference.fasta
-ref proj/reference/reference.fasta The reference genome assembly. If it is
a genbank or embl file, then it will be
converted to reference.gbk.fasta and will
be used for SNP annotation. If a fasta
is given, then no SNP annotation will
happen. Using a gbk or embl file is currently
experimental.
SNP MATRIX OPTIONS
--allowedFlanking 0 allowed flanking distance in bp. Nucleotides this close together cannot be considered as high-quality.
--min_alt_frac 0.75 The percent consensus that needs to be reached before a SNP is called. Otherwise, 'N'
--min_coverage 10 Minimum coverage needed before a SNP is called. Otherwise, 'N'
Where parameters with a / are directories
LOCATIONS OF FILE DIRECTORIES
-reads readsdir/ where fastq and fastq.gz files are located
-bam bamdir/ where to put bams
-vcf vcfdir/ where to put vcfs
--tmpdir tmpdir/ tmp/ Where to put temporary files
--msadir msadir/ multiple sequence alignment and tree files (final output)
--logdir logdir/ Where to put log files. Qsub commands are also stored here.
-asm asmdir/ directory of assemblies. Copy or symlink the reference genome assembly to use it if it is not already in the raw reads directory
PERFORM CERTAIN STEPS
--mask-phages Search for and mask phages in the reference genome
--mask-cliffs Search for and mask 'Cliffs' in pileups
SKIP CERTAIN STEPS
--nomatrix Do not create an hqSNP matrix
--nomsa Do not make a multiple sequence alignment
--notrees Do not make phylogenies
--singleend Treat everything like single-end. Useful for when you think there is a single-end/paired-end bias.
OTHER SHORTCUTS
--fast Shorthand for --downsample --mapper snap --nomask-phages --nomask-cliffs --sample-sites
--presets "" See presets.conf for more information
--downsample Downsample all reads to 50x. Approximated according to the ref genome assembly
--sample-sites Randomly choose a genome and find SNPs in a quick and dirty way. Then on the SNP-calling stage, only interrogate those sites for SNPs for each genome (including the randomly-sampled genome).
MODULES
--read_cleaner none Which read cleaner? Choices: none, CGP, BayesHammer
--mapper smalt Which mapper? Choices: smalt, snap, stampy
--snpcaller varscan Which variant filterer? Choice: varscan, vcftools
SCHEDULER AND MULTITHREADING OPTIONS
--queue all.q The default queue to use.
--numnodes 50 maximum number of nodes
--numcpus 1 number of cpus
--qsubxopts '-N lyve-set' Extra options to pass to qsub. This is not sanitized; internal options might overwrite yours.
See: examples.md for more details.
The script set_manage.pl sets up the project directory and adds reads, and you should use the following syntax. Note that paired end reads should be in interleaved format. Scripts that interleave reads include run_assembly_shuffleReads.pl in the CG-Pipeline package (included with make install) and also shuffleSequences_fastq.pl in the Velvet package.
# Shuffle your reads if they are not shuffled already.
$ shuffleSplitReads.pl some/directory/*.fastq.gz -o interleaved # interleaved directory will be created for you
# Create the project directory `setTest`
$ set_manage.pl --create setTest
# Add reads
$ for i in interleaved/*.fastq.gz; do
> set_manage.pl setTest --add-reads $i
> done;
# Add assemblies (optional)
$ set_manage.pl setTest --add-assembly file1.fasta
$ set_manage.pl setTest --add-assembly file2.fasta
# Specify your reference genome
$ set_manage.pl setTest --change-reference file3.fasta
Run Lyve-SET with as few options as possible
$ launch_set.pl setProj
More complex
$ launch_set.pl setProj --queue all.q --numnodes 20 --numcpus 16 --noclean --notrees
Most output files that you will want to see are under project/msa. However for more details please see docs/output.md.
- Check out the FAQ first to see if your question has already been asked
- Join the Google Group at https://groups.google.com/forum/#!forum/lyve-set
- Tips and tricks
To cite lyve-SET, please reference this site and cite the Haiti Anniversary paper. Lyve-SET also makes use of the tools shown above in the prerequisites. If you feel like your study relied heavily on any of those tools, please don't forget to cite them!
https://github.com/lskatz/lyve-SET
Katz LS, Petkau A, Beaulaurier J, Tyler S, Antonova ES, Turnsek MA, Guo Y, Wang S, Paxinos EE, Orata F, Gladney LM, Stroika S, Folster JP, Rowe L, Freeman MM, Knox N, Frace M, Boncy J, Graham M, Hammer BK, Boucher Y, Bashir A, Hanage WP, Van Domselaar G, Tarr CL.
2013. Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti.
MBio 4(4):e00398-13. doi:10.1128/mBio.00398-13.