Use when converting legacy Novoalign text output into SAM, especially for unique alignments and optional paired-end interpretation.
novo2sam.pl [-p] alignments.novo > alignments.sam/home/vimalinx/miniforge3/envs/bio/bin/novo2sam.pl-p when the Novoalign output contains paired reads.# 1) Convert single-end Novoalign output
novo2sam.pl \
alignments.novo > alignments.sam
# 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
-p only when the file contains paired reads in the expected alternating layout.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.Getopt::Std, so --help works generically but -help is the wrong pattern for this script family.