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What's new in USEARCH version 8

Ultra-fast read mapping >
Map reads to reference genomes at speeds typically ~50x faster than bowtie.
  Enhanced FASTQ support >
Most search and clustering commands now accept FASTQ as well as FASTA files.
Long sequence support >
Chromosome-length sequences are now supported, overcoming a significant limitation in earlier versions of USEARCH.
  Taxonomy assignment >
Ultra-fast taxonomy assignment. Classify millions of reads in a few minutes.
Whole-genome alignment >
USEARCH v8 supports alignments of whole genomes, chromosomes or contigs, from viruses to eukaryotes.
  Agglomerative clustering >
Ultra-fast hierarchical clustering including average linkage (UPGMA), maximum (complete) linkage and minimum (single) linkage.
Rarefaction >
Generate rarefaction curves for standard and non-standard cases, including UPARSE with singletons discarded.
  Distance matrices >
Highly optimized calculation of sparse distance matrices. These can be used to build trees & clusters.
PCR amplicon prediction >
Fast, non-heuristic search for matches to pairs of primers that would generate PCR amplicons.
  Search for short oligos & peptides >
Fast, non-heuristic search for short nucleotide or amino acid sequences, e.g. primers and probes. Degenerate positions (wildcard characters) are supported for oligos.
NAST alignments >
Aligns sequences to an existing reference alignment, keeping the number of columns fixed.
  Fast exact matching >
The new search_exact command is highly optimized for finding exact matches.
SAM file support >
The SAM format is now supported by search and clustering commands that generate alignments.