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fastq_mergepairs options

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.

-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.