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Quick start for USEARCH v7 users
New features
Version 8 is a major re-write of USEARCH. There are many new features, including support for chromosome-length sequences, read mapping, whole-genome alignment, agglomerative clustering, rarefaction, NAST alignments and improved FASTQ support. Now, most search and clustering commands accept FASTQ files as well as FASTA.

For more, see What's new in version 8.

Enhanced UDB file format
Version 8 UDB files are not compatible with v7. If you have both versions installed, one way to deal with this is to use a different filename extension, e.g. db.udb8 for a version 8 database.

Command-line compatibility with v7
Most command lines for v7 should work unchanged in v8. There are a few exceptions, which ideally would be fully documented, but in practice it's not as easy as you might think for me to figure out exactly what they are. If you have existing scripts / pipelines / workflows based on v7, then it is probably best to continue to use v7 in those and use v8 only when you need the new features. See installing multiple versions.

In several cases, including derep_fulllength, derep_prefix, sortbylength and sortbysize, the -output option has been replaced by -fastaout. In future, other types of output may be supported as well, e.g. -fastqout for FASTQ files.

The -usersort option of cluster_smallmem is no longer supported. Instead, you should use -sortedby other.

If an obsolete option is used, a fatal error will occur. If an option is given on the command line but is not used, then a warning message will be issued.

These commands have been replaced: findorfs by fastx_findorfs, maskfasta by fastx_mask.