See also
fastq_mergepairs command
Input files
-fastq_mergepairs
Forward FASTQ filename(s).
-reverse Reverse
FASTQ filename(s). If not given, constructed by replacing R1 with R2.
-interleaved Forward and reverse reads are interleaved in
the same file (sometimes produced by SRA fastq-dump).
Output
files
-fastqout FASTQ filename for merged reads.
-fastaout
FASTA filename for merged reads.
-fastqout_notmerged_fwd FASTQ
filename for forward reads which were not merged.
-fastaout_notmerged_fwd
FASTA filename for forward reads which were not merged.
-fastqout_notmerged_rev
FASTQ filename for reverse reads which were not merged.
-fastaout_notmerged_rev
FASTA filename for reverse reads which were not merged.
Reports
-report Filename for summary report. See
Reviewing a fastq_mergepairs report to check for
problems.
-tabbedout Tabbed text file containing detailed
information about merging process for each pair including reason for discarding.
-alnout Human-readable alignments. Useful for
trouble-shooting.
Merged read labels
-relabel
Prefix string for output labels. The read number 1, 2, 3... is appended after
the prefix.
-relabel @ Relabel using prefix string constructed from
FASTQ filename, this will be understood as the sample identifier.
-sample
xxx Append sample identifier to read label using sample=xxx; format. This is
an alternative method for adding sample ids.
-fastq_eeout Add ee=xxx; annotation with the
number of expected errors in the merged read.
-label_suffix
Suffix to append to merged read label. Can be used e.g. to add sample=xxx; type
of sample identifier annotations.
Filtering
-fastq_maxdiffs
Maximum number of mismatches in the alignment. Default 5. Consider increasing if
you have long overlaps.
-fastq_pctid Minimum %id of alignment. Default
90. Consider decreasing if you have
long overlaps.
-fastq_nostagger Discard
staggered pairs. Default is to trim overhangs
(non-biological sequence).
-fastq_merge_maxee Maximum expected
errors in the merged read. Not recommended for OTU
analysis.
-fastq_minmergelen Minimum length for the merged
sequence. See Filtering artifacts by setting a
merge length range.
-fastq_maxmergelen Maximum length for
the merged sequence.
-fastq_minqual Discard merged read if any
merged Q score is less than the given value. (No minimum
by default).
-fastq_minovlen Discard pair if alignment is
shorter than given value. Default 16.
Pre-processing of reads before alignment
-fastq_trunctail
Truncate reads at the first Q score with <= this value. Default 2.
-fastq_minlen
Discard pair if either read is shorter than this, after truncating by -fastq_trunctail
if applicable. Default 64.
Multi-threading
-threads Specifies the number
of threads. Default 10, or the number of CPU cores, which ever is less.