I have the following tasks that I need to carry out
a. BAM mapping of Illumina HiSeq 4000 paired end 2150bp reads to *de novo assembly inferred from those reads,
b. Sort BAM file by coordinates,
c. Index BAM file,
d. Mark or Remove Duplicates in BAM file.
When I was looking into software to generate my reads <=> assembly BAM file, there are so many options: https://www.ecseq.com/support/ngs/what-is-the-best-ngs-alignment-software
Are there any top recommendation(s) from the community, and rationale behing those recommendations (based on differences amongst this long list of software)?