SWARM 2.1.1

Fix a bug with the fastidious option that caused it to ignore some connections between heavy and light swarms.

swarm 2.1.0

Version 2.1.0 marks the first official release of swarm 2 with a number of improvements and new features:

• built-in breaking phase now performed automatically
• built-in strict dereplication (with d = 0)
• possibility to output OTU representatives in fasta format (option -w)
• fast algorithm now used by default for d = 1 (linear complexity)
• a new option called fastidious that refines d = 1 results and reduces the number of small OTUs

QIIME-ready version 2

Release 1.2.19 brings corrections made to swarm and to the swarm_breaker.py script for a better integration with QIIME.

QIIME-ready version

That new release contains improvements and small modifications made to swarm and to the swarm_breaker.py script for integration into QIIME.

SWARM version 1.2.6

SWARM version 1.2.6 includes an option for producing mothur-compatible output files. Also, this version will provide information about the location and kind of eventual illegal characters encountered in the input fasta file.

SWARM version 1.2.5

This version will run on cpus without the POPCNT feature. Just SSE2 is now required.

SWARM version 1.2.4

Changes the name of the new option to --break-swarms.

SWARM version 1.2.3

Adds the option -b or --break_swarms to output all pairs of amplicons.