-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).
-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.
-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.
-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_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.
-threads Specifies the number of threads. Default 10, or the number of CPU cores, which ever is less.