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).

filter_phix command

Filter reads for hits to the PhiX genome which is used as a spike in Illumina amplicon sequencing.

Input is a FASTA or FASTQ file. A reverse (R2) read file can be specified using -reverse, in which case a read pair is discarded if the forward (R1) and/or reverse (R2) read has a hit to PhiX. If -reverse is specified, -output2 must be specified for the reverse read output file. Output is written in the same format (FASTA or FASTQ) as the input.

Standard output files are supported for reporting PhiX hits.

Multithreading is supported.

Examples

usearch -filter_phix reads.fq -output filtered_reads.fq -alnout hits.txt

usearch -filter_phix reads_fwd.fq -reverse reads_rev.fq -output fil_fwd.fq -output2 fil_rev.fq