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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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SAM file support > The SAM format is now supported by search and clustering commands that generate alignments. |