- Adds translate.seqs command. #789
- Adds make.count command to assign groups to fasta files.
- Adds format parameter to make.group command.
- Updates fastq.info, trim.seqs, trim.flows to output count file by default.
- Significant speed improvements to commands that split by sample. ie, pre.cluster, chimera commands
- Significant speed Improvements to unifrac.weighted.
- Adds group name check to update sample names with illegal characters.
- Adds flow file to get.groups
- General speed improvement with sequence commands.
- Fixes bug with chimera.vsearch with no groups and denovo
- Fixes bug with clearcut sequence name copy
- Fixes bug with make.contigs screening parameters if maxlength not set
- Fixes bug with split.groups flow file option with count table
- Fixes bug with sets parameter not passing to pairwise lefse calc
- Fixes bug with make.sra single-end reads