filter_lowc command
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11-Aug-2018 New paper describes octave plots for visualizing alpha diversity.

12-Jun-2018 New paper shows that one in five taxonomy annotations in SILVA and Greengenes are wrong.

18-Apr-2018 New paper shows that taxonomy prediction accuracy is <50% for V4 sequences.

05-Oct-2017 PeerJ paper shows low accuracy of closed- and open-ref. QIIME OTUs.

22-Sep-2017 New paper shows 97% threshold is wrong, OTUs should be 99% full-length 16S, 100% for V4.

UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.



filter_lowc command

See also
Quality control for OTU sequences

Filter low-complexity sequences.

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 is found to be low-complexity. 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.

A sequence is discarded if it is >25% low-complexity. This threshold can be changed with the max_lowc_pct option.

The -hitsout file contains the low-complexity sequences that were removed.

The -tabbedout file species an output file in tabbed text format which reports the percentage of low complexity sequence found in each of the query sequences.

Multithreading is supported.


usearch -filter_lowc reads.fq -output filtered_reads.fq -tabbedout lowc.txt -hitsout lowc.fq

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