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derep_fulllength Find unique sequences and abundances (old name for fastx_uniques)
fastq_chars Reports frequencies of Phred (Q) scores in FASTQ file
fastq_eestats Expected error distribution in FASTQ file (long report)
fastq_eestats2 Expected error distribution in FASTQ file (short report)
fastq_filter Quality filter FASTQ and/or convert reads to FASTA format.
fastq_join Concatenate forward (R1) and reverse (R2) reads
fastq_mergepairs Merge (assemble) paired reads with overlaps
fastq_sra_splitpairs Recover R1 and R2 reads from SRA interleaved or concatenated format
fastx2qiime Convert sample names to QIIME-compatible format
fastx_demux Assign reads to samples using index reads (demultiplex)
fastx_learn Estimate error rates for amplicon reads
fastx_revcomp Reverse-complement nucleotide sequences
fastx_split Split FASTX file into two or more roughly equal-size pieces
fastx_strip_annots Strip annotations from labels
fastx_subsample Extract random subset of sequences in a FASTX file
fastx_truncate Truncate sequences
fastx_uniques Find unique sequences and abundances
fastx_uniques_persample Find unique sequences and abundances per sample
filter_phix Filter PhiX sequences
orient Orient nt sequences to the same strand as a database
sortbylength Sort by decresing sequence length
sortbysize Sort by decresing abundance (size= annotations)
unoise3 Correct errors (denoise) amplicon reads, includes chimera filter