Video talks on 16S data analysis posted.

URMAP ultra-fast read mapper posted (paper).

~20% of taxonomy annotations in SILVA and Greengenes are wrong (paper).

Taxonomy prediction is <50% accurate for 16S V4 sequences (paper).

97% OTU threshold is wrong for species, should be 99% for full-length 16S, 100% V4 (paper).

findorfs command

The fastx_findorfs command finds ORFs in nucleotide sequences in a FASTA or FASTQ file.

The -orfstyle and -mincodons options control ORF identification. The -output option specifies the output filename.

The -ntout output file is a FASTA filename for nucleotide sequences.

The -aaout output file is a FASTA filename for translated (amino acid) sequences.

Example

usearch -fastx_findorfs reads.fastq -ntout -nt.fa -aaout aa.fa -orfstyle 7 -mincodons 16