Quick start for USEARCH v7 users
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
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.
cases, including derep_fulllength,
sortbysize, the -output option has been replaced by -fastaout.
In future, other types of output may be supported as well, e.g. -fastqout for
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