Performs merging of paired reads. (This is
sometimes called 'assembly' of paired reads, but I find this term confusing
because assembly usually refers to making longer contigs, so I prefer to call it
merging).
The FASTQ
filename for the forward reads is specified by the -fastq_mergepairs option, and
the reverse read filename is specified by the -reverse option. Output files are
specified by -fastqout (for FASTQ) and / or -fastaout (for FASTA).
Forward and reverse must be in 1:1 correspondence and
must appear in the same order in both files. The labels for the forward and
reverse read in a given pair must be identical except for a single position
where a '1' appears in the forward read label and a '2' appears in the reverse
read label.
See also
FASTQ files
Quality scores
FASTQ format options
| Option |
|
Description |
|
fastq_minovlen k |
|
Minimum length of the overlap. Default: no minimum.
Note: overlaps shorter than the -minhsp
option will fail to align, so this option also has the effect of imposing a
minimum overlap. You should therefore set -minhsp to the shortest overlap that
you expect in your data. Values less than 8 may cause performance problems, and
may cause spurious overlaps.
|
|
fastq_minmergelen L |
|
Minimum length of the merged read. Default: no maximum.
|
|
fastq_maxmergelen L |
|
Maximum length of the merged read. Default: no maximum.
|
|
fastq_maxdiffs d |
|
Maximum number of mismatches allowed in the overlap
region. Default: any number of mismatches allowed.
|
|
fastq_truncqual q |
|
Truncate the forward and reverse reads at the first Q<=q,
if present. This truncation is performed before aligning the pair. With Illumina
paired reads, it is recommended to use ‑fastq_trunqual 2 or higher, as
low-quality tails will otherwise often cause alignment of the pair to fail.
Default: no quality truncation.
|
|
fastq_minlen L |
|
Minimum length of the forward and reverse read, after
truncating per ‑fastq_truncqual if applicable. Default: no minimum.
|
|
fastq_allowmergestagger |
|
Allow merge of a pair where the alignment is "staggered"
like this: --FORWARD
REVERSE--
By default, pairs with staggered alignments are
discarded.
|
Example
usearch -fastq_mergepairs fwd.fastq -reverse rev.fastq -fastq_truncqual 3 \
-fastq_maxdiffs 0 -fastqout merged.fastq
|