mashtree
Create a tree using Mash distances.
For simple usage, see mashtree.pl. For advanced options, look at mashtree_wrapper.pl.
Examples
mashtree.pl --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.
Advanced
mashtree_wrapper.pl --reps 100 -- --numcpus 12 *.fastq.gz > mashtree.dnd
Usage
mashtree.pl: use distances from Mash (min-hash algorithm) to make a NJ tree
Usage: mashtree.pl [options] *.fastq *.fasta *.gbk > 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 not specified, one 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
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
Also see mashtree_wrapper.pl for advanced usage. Run either script with
--help for additional information.
Requirements
- Mash >= v1.1
- SQLite3
- Perl
- multithreading
- BioPerl library
DBD::SQLite
Installation
After downloading the latest release, go into the directory and run make
$ cd mashtree
$ perl Makefile.PL
$ make test
Add mashtree/bin to PATH and you're good to go!
References
- Mash: http://mash.readthedocs.io
- BioPerl: http://bioperl.org
GitHub stickers for Mashtree
