The results of short read alignments are very commonly summarized and output in the form of SAM (Sequence Alignment Map) files, or BAM files (the compressed, binary equivalent of SAM). These files should contain all of the information you need for downstream analyses such as annotation, transcript abundance comparisons, and polymorphism detection.

SAMtools is used to sort and index alignments in order to support a faster and less memory intensive alignment by the STAR or Kallisto tools used downstream.

References:

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PMID: 19505943

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