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LYVE version of the Snp Extraction Tool (SET), a method of using hqSNPs to create a phylogeny.

Main tool: Lyve-SET

Additional tools:

  • ncbi-blast+ 2.2.31
  • python 2.7.12
  • python 3.5.2
  • bioperl 1.6.924
  • cpanminus 1.7040
  • NCBI E-utilities
  • Git 2.7.4
  • VCFTools 0.1.12b
  • SAMTools 1.2
  • VarScan 2.3.7
  • BCFTools 1.3.1
  • SMALT 0.7.6
  • SNAP 1.0beta.18
  • RAxML 8.1.16
  • Quake 0.3.5

Example Usage

Help:

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

Analyze test data:

set_test.pl --numcpus 8 lambda lambda

Analyze your data:

set_manage.pl --create yourProject
# paired end reads have to be shuffled into one file per sample
shuffleSplitReads.pl --numcpus 8 -o interleaved *.fastq.gz
# then moved into your project dir
mv interleaved/*.fastq.gz yourProject/reads/
# cleanup
rmdir interleaved
cp reference.fasta yourProject/ref/
launch_set.pl --numcpus 8 -ref yourProject/ref/reference.fasta yourProject