See also
OTU / denoising
pipeline
Read preparation
Paired read merging
Edgar & Flyvbjerg 2014 paper on expected errors and
Bayesean assembly
If you have paired reads, pick a couple of samples and try running the
fastq_mergepairs command. Verify
that most of the pairs align and that the lengths of the consensus sequences
are consistent with the distribution expected for your primer pair. See
links from the fastq_mergepairs command
page for more documentation about adjusting parameters, verifying the
results and trouble-shooting problems.
Paired read merging should be performed before
quality filtering because merging improves base call error
estimates (Q scores) in the overlapping
segment.
Example, 2x250
V4
With very long overlaps such as typical 2x250 V4 you will sometimes find
that it is better to allow more differences in the alignment compared to the
default parameters; see
example report. For example, you might
choose to increase set -fastq_maxdiffs 10 -fastq_pctid 80:
usearch -fastq_mergepairs *R1*.fastq -relabel @ -fastq_maxdiffs 10 -fastq_pctid
80 \
-fastqout merged.fq
This command uses a couple of convenient features supported by
fastq_mergepairs: merging several samples into one file by using shell
wildcards (*R1*), and automatically embedding the sample name into the read
label by using -relabel @.