mashtree *.fastq.gz > tree.dnd

mashtree --numcpus 12 *.fastq.gz [*.fasta] > mashtree.dnd

mashtree --mindepth 0 --numcpus 12 *.fastq.gz [*.fasta] > mashtree.dnd

mashtree_jackknife.pl --reps 100 --numcpus 12 *.fastq.gz -- --min-depth 0 > mashtree.jackknife.dnd
mashtree_jackknife.pl --help # additional usage help

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