mashtree
Create a tree using Mash distances.
For simple usage, see mashtree.pl
. For advanced options, look at mashtree_wrapper.pl
.
Examples
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.
Advanced
mashtree_wrapper.pl --reps 100 -- --numcpus 12 *.fastq.gz > mashtree.dnd
Usage
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.
Requirements
- Mash >= v1.1
- SQLite3
- Perl
- multithreading
- BioPerl library
DBD::SQLite
Installation
Installation from Git
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!
Installation from CPAN
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
Alternate method of installing from CPAN
$ 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
Uninstallation from CPAN
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
References
- Mash: http://mash.readthedocs.io
- BioPerl: http://bioperl.org