Create a tree using Mash distances.
For simple usage, see mashtree.pl. For advanced options, look at mashtree_wrapper.pl.
mashtree.pl --numcpus 12 *.fastq.gz [*.fasta] > mashtree.dnd Note: fastq files are interpreted as raw read files. Fasta, GenBank, and EMBL files are interpreted as genome assemblies.
Note: Compressed files are also accepted of any of the above file types. You can compress with gz, bz2, or zip.
mashtree_wrapper.pl --reps 100 -- --numcpus 12 *.fastq.gz > mashtree.dnd Usage: mashtree.pl [options] *.fastq *.fasta *.gbk *.msh > tree.dnd NOTE: fastq files are read as raw reads; fasta, gbk, and embl files are read as assemblies; Input files can be gzipped. --tempdir '' If specified, this directory will not be removed at the end of the script and can be used to cache results for future analyses. If not specified, a dir will be made for you and then deleted at the end of this script. --numcpus 1 This script uses Perl threads. --outmatrix '' If specified, will write a distance matrix in tab-delimited format --version Display the version and exit TREE OPTIONS --truncLength 250 How many characters to keep in a filename --sort-order ABC For neighbor-joining, the sort order can make a difference. Options include: ABC (alphabetical), random, input-order MASH SKETCH OPTIONS --genomesize 5000000 --mindepth 5 If mindepth is zero, then it will be chosen in a smart but slower method, to discard lower-abundance kmers. --kmerlength 21 --sketch-size 10000 Also see mashtree_wrapper.pl for advanced usage. Run either script with --help for additional information.
- Mash >= v1.1 - please upgrade to v2.0 for future releases of Mashtree.
- SQLite3
- Perl
- multithreading
- BioPerl library
DBD::SQLite
- QuickTree - makes tree inference about 100x faster.
After downloading the latest release, go into the directory and run make
$ cd mashtree $ perl Makefile.PL $ make test Add mashtree/bin to PATH and you're good to go!
Installing from CPAN installs the latest stable version of Mashtree. This method should add the Mashtree perl modules to the correct place in your home directory and should add the executables to your local bin directory. However, I am new to CPAN, so please give me feedback via the issues tab if this is not correct.
$ cpanm -L ~ Mashtree $ export PERL5LIB=$PERL5LIB:$HOME/lib/perl5 $ mashtree.pl --help # verify it shows usage and not an error $ cpan # initiates the CPAN command line prompt cpan[1]> install Mashtree cpan[2]> exit $ export PERL5LIB=$PERL5LIB:$HOME/lib/perl5 $ mashtree.pl --help # verify it shows usage and not an error I'm not sure why you'd want to uninstall Mashtree but here is how you would clean it up.
$ cpanm --uninstall Mashtree --local-lib=$HOME - Mash: http://mash.readthedocs.io
- BioPerl: http://bioperl.org
