VSEARCH 2.13.4

Added information about support for gzip- and bzip2-compressed input files to the output of the version command. Adapted source code for compilation on FreeBSD and NetBSD systems.

VSEARCH 2.13.3

Fix bug in FASTQ parsing introduced in version 2.13.2.

VSEARCH 2.13.1

Minor changes to the allowed options for each command. All commands now allow the log, quiet and threads options. If more than 1 thread is specified for commands that are not multi-threaded, a warning will be issued. Minor changes to the manual.

VSEARCH 2.13.0

Added the fastx_getseq, fastx_getseqs and fastx_getsubseq commands to extract sequences from a FASTA or FASTQ file based on their labels. Improved handling of ambiguous nucleotide symbols. Corrected behaviour of uchime_ref command with and options self and selfid. Strict detection of illegal options for each command.

VSEARCH 2.12.0

Take sequence abundance into account when computing consensus sequences or profiles after clustering. Warn when rereplicating sequences without abundance info. Guess offset 33 in more cases with fastq_chars. Stricter checking of option arguments and option combinations.

VSEARCH 2.11.1

Minor change to the handling of the weak_id and id options when using cluster_unoise.

VSEARCH 2.11.0

Added ability to trim and filter paired-end reads using the reverse option with the fastx_filter and fastq_filter commands. Added xee option to remove ee attributes from FASTA headers. Minor invisible improvement to the progress indicator.

VSEARCH 2.10.4

Fixed serious bug in x86_64 SIMD alignment code introduced in version 2.10.3. Added link to BioConda in README. Fixed bug in fastq_stats with sequence length 1. Fixed use of equals symbol in UC files for identical sequences with cluster_fast.

VSEARCH 2.10.2

Fix bug in sintax with reversed order of domain and kingdom.

VSEARCH 2.10.1

Improved sff_convert command. It will now read several variants of the SFF format. It is also able to read from a pipe. Warnings are given if there are minor problems. Errors messages have been improved. Minor speed and memory usage improvements.