mashtree
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.
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.
See the documentation on the algorithms for more information.
Faster
mashtree --numcpus 12 *.fastq.gz [*.fasta] > mashtree.dnd
More accurate
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
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
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
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
Installation
Please see INSTALL.md
Further documentation
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.
References
- Mash: http://mash.readthedocs.io
- BioPerl: http://bioperl.org
Citation
JOSS
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
Poster
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.
