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.

lskatz / mashtree

readme