Create a tree using Mash distances.
For simple usage, see mashtree --help. This is an example command:
mashtree *.fastq.gz > tree.dnd For confidence values, run either with --help: mashtree_bootstrap.pl or mashtree_jackknife.pl.
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.
See the documentation on the algorithms for more information.
mashtree --numcpus 12 *.fastq.gz [*.fasta] > mashtree.dnd You can get a more accurate tree with the minimum abundance finder. Simply give --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 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 flags to 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 Please see INSTALL.md
For perl library help, run perldoc on a .pm file, e.g., perldoc lib/Mashtree/Db.pm.
For executable help run --help, e.g., mashtree_bootstrap.pl --help.
For more information and help please see the docs folder
For more information on plugins, see the plugins folder. (in development)
For more information on contributions, please see CONTRIBUTING.md.
- Mash: http://mash.readthedocs.io
- BioPerl: http://bioperl.org
Katz, L. S., Griswold, T., Morrison, S., Caravas, J., Zhang, S., den Bakker, H.C., Deng, X., and Carleton, H. A., (2019). Mashtree: a rapid comparison of whole genome sequence files. Journal of Open Source Software, 4(44), 1762, https://doi.org/10.21105/joss.01762
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. Poster number 27.
