See also
FASTQ files
Quality scores
FASTQ format options
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 (called R1 by Illumina) is specified by the -fastq_mergepairs option, and
the reverse read filename (called R2 by Illumina) is specified by the ‑reverse option.
Merged reads are written to -fastqout (for FASTQ) and / or -fastaout (for FASTA).
Reads which failed to merge are written to ‑fastqout_notmerged_fwd,
-fastqout_notmerged_rev, -fastaout_notmerged_fwd,
-fastaout_notmerged_rev. The ‑eetabbedout.output
file is a tabbed text file given expected and observed errors in the read pair.
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.
The -label_suffix option specifies a string that is
appended to the labels of the merged reads.
| 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 minimum.
|
|
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_maxgaps n |
|
(v8.0.1616 or later). Maximum number of gaps allowed in the alignment of the
overlapping region. Default is 0, because gaps are very rare with Illumina
paired reads so gaps are more likely to indicate a misalignment than a read
error. Also, the merge is ambiguous in a gapped column: should the base be
included or not? There is no Q score to decide which read is better in this
case.
|
|
fastq_maxee e |
|
Discard pairs if the number of
expected errors is > e after merging. By default, no expected error
filtering is performed. (Requires v8.0.1610 or later. In earlier versions, you
can use fastq_filter to perform e.e.
filtering on the merged reads).
|
|
fastq_truncqual q |
|
This option is provided for older Illumina data with "#"
tails, it is not recommended for newer reads.
It truncates the forward and reverse reads at the first Q<=q,
if present. This truncation is performed before aligning the pair. This option
is provided for older Illumina reads where Q=2 was used to indicate a bad tail.
For such reads, it is recommended to use ‑fastq_trunqual 2 or higher, as
low-quality tails often caused alignments to fail. Default: no quality
truncation as this is not needed with newer reads.
|
|
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.
You should always use -fastq_trimstagger if you
allow staggered alignments; I don't know of any
scenario where you want to keep the overhangs.
|
|
fastq_trimstagger |
|
Delete "overhangs" in a staggered alignment. In the above
example, this would discard RE at the start and RD at the end. In v8.0.1610 and
later, staggered alignments are always trimmed and -fastq_trimstagger is
ignored.
|
fastqout_notmerged_fwd
fastqout_notmerged_rev
fastaout_notmerged_fwd
fastaout_notmerged_rev
|
|
Filenames for forward and reverse reads that are not
merged (FASTQ or FASTA format). |
|
fastq_eeout |
|
Append "ee=xxx;" annotation to the read labels giving the
expected errors after merging. (Requires v8.0.1610
or later).
|
|
alnout |
|
Alignments in human-readable format. (Requires v8.0.1610
or later).
|
Example
usearch -fastq_mergepairs fwd.fastq -reverse rev.fastq
-fastqout merged.fastq \
-fastq_merge_maxee 1.0
|