Create a tree using Mash distances.
For simple usage, see
mashtree. For advanced options, look at
mashtree --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.
Slow and more accurate
You can get a more accurate tree with the minimum abundance finder. Simply
--mindepth 0. This step helps ignore very unique kmers that are
more likely read errors.
mashtree --mindepth 0 --numcpus 12 *.fastq.gz [*.fasta] > mashtree.dnd
mashtree_wrapper.pl --reps 100 -- --numcpus 12 *.fastq.gz > mashtree.dnd
Usage: mashtree [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 --outtree If specified, the tree will be written to this file and not to stdout. Log messages will still go to stderr. --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
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.
- BioPerl library
- Quicktree. Note: Quicktree version 2.3 has been redistributed in this repo. This version of Quicktree has been modified to increase the precision from 5 digits to 10 digits.
Installation from Git
After downloading the latest release, go into the directory and run
$ cd mashtree $ perl Makefile.PL $ make test
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 --help # verify it shows usage and not an error
Alternate method of installing from CPAN
$ cpan # initiates the CPAN command line prompt cpan> install Mashtree cpan> exit $ export PERL5LIB=$PERL5LIB:$HOME/lib/perl5 $ mashtree --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
For more information please see the docs folder
For more information on plugins, see the plugins folder.
The paper is in preparation but for now, this is a valid citation:
Katz, L. S., Griswold, T., & Carleton, H. A. (2017, October 8-11). Generating WGS Trees with Mashtree. Poster presented at the American Society for Microbiology Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines, Washington, DC.