Novo2sam Pl

# 2) Convert paired-end Novoalign output
novo2sam.pl \
  -p \
  paired_alignments.novo > paired.sam

# 3) Stream a filtered Novoalign file through the converter
grep -v '^#' alignments.novo | novo2sam.pl > alignments.sam

Recommended Workflow

1. Confirm the input is Novoalign's legacy text alignment format rather than already-formed SAM/BAM.
2. Enable -p only when the file contains paired reads in the expected alternating layout.
3. Convert to SAM, then inspect a few records for pairing flags, CIGAR strings, and sequence orientation.
4. If you need non-unique or QC-failed rows preserved, verify the converter's filtering behavior before trusting the output.

Guardrails

• The script silently skips lines it considers QC/NM summary output and ignores alignments whose status field is not U (unique), so it is not a lossless converter for all Novoalign record types.
• -p changes mate interpretation only; it does not repair arbitrarily shuffled paired-end records.
• Help comes from Perl Getopt::Std, so --help works generically but -help is the wrong pattern for this script family.
• Output is plain SAM records without a SAM header.