From 87547da697a6e622f0d9c9556c80118aee2564bd Mon Sep 17 00:00:00 2001 From: Lee Katz Date: Sat, 15 Oct 2022 00:59:14 -0400 Subject: [PATCH] mashtree: add page (#8938) --- pages/linux/mashtree.md | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 pages/linux/mashtree.md diff --git a/pages/linux/mashtree.md b/pages/linux/mashtree.md new file mode 100644 index 000000000..224c2e2a5 --- /dev/null +++ b/pages/linux/mashtree.md @@ -0,0 +1,17 @@ +# mashtree + +> Makes a fast tree from genomes. +> Does not make a phylogeny. +> More information: . + +- 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}}`