Update cheatsheets

linux/mashtree

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+---
+syntax: markdown
+tags: [tldr, linux]
+source: https://github.com/tldr-pages/tldr.git
+---
+# mashtree
+
+> Makes a fast tree from genomes.
+> Does not make a phylogeny.
+> More information: <https://github.com/lskatz/mashtree>.
+
+- Fastest method in mashtree to create a tree from fastq and/or fasta files using multiple threads, piping into a newick file:
+
+`mashtree --numcpus {{12}} {{*.fastq.gz}} {{*.fasta}} > {{mashtree.dnd}}`
+
+- Most accurate method in mashtree to create a tree from fastq and/or fasta files using multiple threads, piping into a newick file:
+
+`mashtree --mindepth {{0}} --numcpus {{12}} {{*.fastq.gz}} {{*.fasta}} > {{mashtree.dnd}}`
+
+- Most accurate method to create a tree with confidence values (note that any options for `mashtree` itself has to be on the right side of the `--`):
+
+`mashtree_bootstrap.pl --reps {{100}} --numcpus {{12}} {{*.fastq.gz}} -- --min-depth {{0}} > {{mashtree.bootstrap.dnd}}`