Bismark Alignment with bowtie2

Option	Functionality
-q	Quiet mode: suppresses detailed output.
--score-min L,0,-0.2	Sets a linear minimum score for valid alignments (moderate stringency).
--ignore-quals	Ignores base quality scores during alignment.
--no-mixed	Ensures both ends of paired reads align properly; no single-end alignments.
--no-discordant	Prevents discordant alignments; enforces proper orientation and distance.
--dovetail	Allows overlapping or extended alignments in paired-end reads.
--maxins 500	Sets the maximum allowed distance between paired-end reads to 500 bases.