I want to make a pipeline that can take sam files from different aligners like HISAT2. One thing I like about HISAT2 is you can either map the reads to a transcripts or a GTF file if you had one available. What I like about BBMAP is that it has
minid=0.76 Approximate minimum alignment identity to look for. Higher is faster and less sensitive.
CLC (a proprietary tool) has
lengthfraction but I'm wondering if there are any downstream tools that can do this from the sam/bam file that is also computationally efficient. If I wrote something in Python it would take a long time (plus I don't really know what I'm doing for this type of work...I deal mostly with downstream data)
-s --similarity Set similarity score (default 0.8).
-l --lengthfraction Set length fraction (default 0.5).
Is there a tool that takes in
sam/bam as input and take parameters like
CLC) that outputs a filtered