Forward FASTQ filename(s).
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).
-fastqout FASTQ filename for merged reads.
FASTA filename for merged reads.
filename for forward reads which were not merged.
FASTA filename for forward reads which were not merged.
FASTQ filename for reverse reads which were not merged.
FASTA filename for reverse reads which were not merged.
-report Filename for summary report. See
Reviewing a fastq_mergepairs report to check for
-tabbedout Tabbed text file containing detailed
information about merging process for each pair including reason for discarding.
-alnout Human-readable alignments. Useful for
Merged read labels
Prefix string for output labels. The read number 1, 2, 3... is appended after
-relabel @ Relabel using prefix string constructed from
FASTQ filename, this will be understood as the sample identifier.
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.
Suffix to append to merged read label. Can be used e.g. to add sample=xxx; type
of sample identifier annotations.
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
staggered pairs. Default is to trim overhangs
-fastq_merge_maxee Maximum expected
errors in the merged read. Not recommended for OTU
-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
-fastq_minovlen Discard pair if alignment is
shorter than given value. Default 16.
Pre-processing of reads before alignment
Truncate reads at the first Q score with <= this value. Default 2.
Discard pair if either read is shorter than this, after truncating by -fastq_trunctail
if applicable. Default 64.
-threads Specifies the number
of threads. Default 10, or the number of CPU cores, which ever is less.