In current genome era, our day to day work is to handle the huge geneome sequences, expression data, several other datasets. This link provide a comprehensive list of commonly used sofware/tools.
That list contains only a subset of software that produces or processes SAM files. There far more comprehensive lists:
Yep, actually there is a relevant topic from omicstools (Omictools: A didactic directory for omic data analysis (NGS, microarray, PCR, MS, NMR)) here
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