Matthew Nitschke nitschkematthew

Symbiotic microbes / ecophysiology / bioinformatics / rstats

ConstantinoSchillebeeckx / vsearch_pick_open_reference_otus.sh

Last active July 28, 2017 09:30

bash script that uses vsearch to run the equivalent of QIIME's pick_open_reference_otus.py

	#!/bin/bash

	echo "Vsearch started: $(date)";
	echo "";

	# generate all the proper directories
	mkdir -p step1_otus; mkdir -p step2_otus; mkdir -p step3_otus; mkdir -p step4_otus

	# must sort because searching done greedily
	# see http://drive5.com/usearch/manual/uparseotu_algo.html