Add script for sketching

CITATION.cff

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+cff-version: 1.2.0
+message: "If you use Bactopia, please cite it as below."
+authors:
+- family-names: "Petit III"
+  given-names: "Robert A. "
+  orcid: "https://orcid.org/0000-0002-1350-9426"
+- family-names: "Read"
+  given-names: "Timothy D."
+  orcid: "https://orcid.org/0000-0001-8966-9680"
+title: "Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes. mSystems. 5 (2020)"
+doi: 10.1128/mSystems.00190-20
+url: "https://github.com/bactopia/bactopia"
+version: 1.4.1

bin/bactopia-sketcher

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+#! /bin/bash
+VERSION=1.0.0
+PREFIX=$1
+FASTQ=$2
+
+# If no user input, print usage
+if [[ $# == 0 ]]; then
+    echo "bactopia-sketcher - v${VERSION}"
+    echo ""
+    echo "bactopia-sketcher <PREFIX> <FASTQ> <OPT1> ... <OPTN>"
+    echo ""
+    exit
+fi
+
+gzip -cd ${FASTQ} | mash sketch -o ${PREFIX}-k21 -k 21 -s 21 -r -I ${PREFIX} -
+gzip -cd ${FASTQ} | mash sketch -o ${PREFIX}-k31 -k 31 -s 31 -r -I ${PREFIX} -
+sourmash sketch dna -p k=21,k=31,k=51,abund,scaled=1000 --merge ${PREFIX} -o ${PREFIX}.sig ${FASTQ}