diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..7157760 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,13 @@ +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 diff --git a/bin/bactopia-sketcher b/bin/bactopia-sketcher new file mode 100755 index 0000000..a47d28e --- /dev/null +++ b/bin/bactopia-sketcher @@ -0,0 +1,17 @@ +#! /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 ... " + 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}