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).

fastx_getlabels command

Writes the sequence labels from a FASTQ or FASTA file to a text file with one label per line. The output file name is given by the -output option.

With FASTA format, the effect is essentially the same as:

grep "^>" input.fa | sed "-es/^>//" > labels.txt

With FASTQ format, there is no simple way to do this using Linux commands because the Q score sequence can start with the same character(s) as a read label.

Example

usearch -fastx_getlabels reads.fq -output labels.txt