vsearch(1) on Linux
The text 02299783b362, as Debian 10 (Buster) shipped it.
chimera detection, clustering, dereplication and rereplication, FASTA/FASTQ file processing, masking, pairwise alignment, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicons for metagenomics, genomics, and population genetics.
Flags it lists
-
--acceptall -
--bzip2_decompress -
--clusterout_id -
--clusterout_sort -
--cons_truncate -
--dbmask -
--eeout -
--fasta_score -
--fastq_allowmergestagger -
--fastq_eeout -
--fastq_join -
--fastq_maxdiffpct -
--fastq_maxee -
--fastq_maxee_rate -
--fastq_mergepairs -
--fastq_nostagger -
--fastq_truncee -
--fulldp -
--gzip_decompress -
--hardmask -
--help -
--iddef -
--join_padgap -
--join_padgapq -
--label_suffix -
--leftjust -
--match -
--mismatch -
--no_progress -
--notrunclabels -
--output_no_hits -
--pattern -
--qmask -
--quiet -
--relabel_keep -
--relabel_md5 -
--relabel_sha1 -
--rightjust -
--samheader -
--sample_pct -
--self -
--selfid -
--sff_clip -
--sintax_cutoff -
--sizein -
--sizeorder -
--sizeout -
--strand -
--top_hits_only -
--uc_allhits -
--uchimeout5 -
--unoise_alpha -
--usersort -
--version -
--xsize -
-h -
-v