Create a tree using Mash distances.
For simple usage, see
mashtree. For advanced options, look at
Two modes: fast or accurate
Input files: fastq files are interpreted as raw read files. Fasta, GenBank, and EMBL files are interpreted as genome assemblies. Compressed files are also accepted of any of the above file types. You can compress with gz, bz2, or zip.
Output files: Newick (.dnd). If
--outmatrix is supplied, then
a distance matrix too.
mashtree --numcpus 12 *.fastq.gz [*.fasta] > mashtree.dnd
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
Adding confidence values
Mashtree can add confidence values using jack knifing. For each
jack knife tree, 50% of hashes are used. Confidence values are calculated from
the jack knife trees using BioPerl. When using this method, you can pass
mashtree using the double-dash like in the example below.
Added in version 0.40.
mashtree_jackknife.pl --reps 100 --numcpus 12 *.fastq.gz -- --min-depth 0 > mashtree.jackknife.dnd mashtree_jackknife.pl --help # additional usage help
Bootsrapping was added in version 0.55. This runs mashtree itself multiple times, each with a random seed.
mashtree_bootstrap.pl --reps 100 --numcpus 12 *.fastq.gz -- --min-depth 0 > mashtree.bootstrap.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 --file-of-files If specified, mashtree will try to read filenames from each input file. The file of files format is one filename per line. This file of files cannot be compressed. --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 >= v2.0
- BioPerl library
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
$ perl -MCPAN -e shell # 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 and help please see the docs folder
For more information on plugins, see the plugins folder. (in development)
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.