A robust and fast clustering method for amplicon-based studies
swarm 3.1.5 fixes four minor bugs, improves code and documentation, and eliminates compilation warnings and static analysis warnings:
shadow
, useless-cast
, conversion
, sign-conversion
),alloc-dealloc
-mismatch, and allocating too much memory; bugs had no impact on clustering results),--network_file
(advanced users),swarm version 3.1.4 fixes a minor bug, eliminates compilation warnings and static analysis warnings, and improves code:
-DNDEBUG
the default compilation behavior,Version 3.1.3 fixes a few minor bugs, removes warnings, and improves code and documentation:
Fix a bug with fastidious mode introduced in version 3.1.1, that could cause Swarm to crash. Probably due to allocating too much memory.
Version 3.1.1 eliminates a risk of segmentation fault with extremely long sequence headers. Documentation and error messages have been improved, and code cleaning continued.
swarm 3.1.0: Improved code and documentation, bugfix, and macOS on ARM64
Version 3.0.0 introduces a faster algorithm for d = 1, and a reduced memory footprint. Swarm has been ported to Windows x86-64, GNU/Linux ARM64, and GNU/Linux POWER8. Internal code has been modernized, hardened, and thoroughly tested. Strict dereplication of input sequences is now mandatory. The --seeds
option (-w
) now outputs results sorted by decreasing abundance, and then by alphabetical order of sequence labels.
Swarm 2.2.2 fixes a bug with an endless wait in rare cases with multiple threads.
Swarm 2.2.1 fixes a memory allocation bug for d=1 that should only affect cases where the input sequences have not ben fully dereplicated.
Version 2.2.0 fixes several problems and improves usability. Corrected output to structure and uclust files when using fastidious mode. Corrected abundance output in some cases. Added check for duplicated sequences and fixed check for duplicated sequence IDs. Checks for empty sequences. Sorts sequences by additional fields to improve stability. Improves compatibility with compilers and operating systems. Outputs sequences in upper case. Allows 64-bit abundances. Shows message when waiting for input from stdin. Improves error messages and warnings. Improves checking of command line options. Fixes remaining errors reported by test suite. Updates documentation.