Swarm 2.1.12 [Jan 18 2017 08:06:54] Copyright (C) 2012-2017 Torbjorn Rognes and Frederic Mahe https://github.com/torognes/swarm Mahe F, Rognes T, Quince C, de Vargas C, Dunthorn M (2014) Swarm: robust and fast clustering method for amplicon-based studies PeerJ 2:e593 https://doi.org/10.7717/peerj.593 Mahe F, Rognes T, Quince C, de Vargas C, Dunthorn M (2015) Swarm v2: highly-scalable and high-resolution amplicon clustering PeerJ 3:e1420 https://doi.org/10.7717/peerj.1420

Swarm 2.1.12 [Jan 18 2017 08:06:54] Copyright (C) 2012-2017 Torbjorn Rognes and Frederic Mahe https://github.com/torognes/swarm Mahe F, Rognes T, Quince C, de Vargas C, Dunthorn M (2014) Swarm: robust and fast clustering method for amplicon-based studies PeerJ 2:e593 https://doi.org/10.7717/peerj.593 Mahe F, Rognes T, Quince C, de Vargas C, Dunthorn M (2015) Swarm v2: highly-scalable and high-resolution amplicon clustering PeerJ 3:e1420 https://doi.org/10.7717/peerj.1420 Usage: swarm [OPTIONS] [filename] General options: -h, --help display this help and exit -t, --threads INTEGER number of threads to use (1) -v, --version display version information and exit Clustering options: -b, --boundary INTEGER min mass of large OTU for fastidious (3) -c, --ceiling INTEGER max memory in MB used for fastidious -d, --differences INTEGER resolution (1) -f, --fastidious link nearby low-abundance swarms -n, --no-otu-breaking never break OTUs -y, --bloom-bits INTEGER bits used per Bloom filter entry (16) Input/output options: -a, --append-abundance INTEGER value to use when abundance is missing -i, --internal-structure FILENAME write internal swarm structure to file -l, --log FILENAME log to file, not to stderr -o, --output-file FILENAME output result filename (stdout) -r, --mothur output in mothur list file format -s, --statistics-file FILENAME dump OTU statistics to file -u, --uclust-file FILENAME output in UCLUST-like format to file -w, --seeds FILENAME write seed seqs with abundances to FASTA -z, --usearch-abundance abundance annotation in usearch style Pairwise alignment advanced options: -m, --match-reward INTEGER reward for nucleotide match (5) -p, --mismatch-penalty INTEGER penalty for nucleotide mismatch (4) -g, --gap-opening-penalty INTEGER gap open penalty (12) -e, --gap-extension-penalty INTEGER gap extension penalty (4) See 'man swarm' for more details.