Analysis Methods | Isaac Aligner | Alignment Output

Alignment Output

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After sorting the reads, the Isaac Aligner generates compressed binary alignment output files, called BAM (*.bam) files, using the following process:

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Marking duplicates—Detection of duplicates is based on the location and observed length of each fragment. The Isaac Aligner identifies and marks duplicates even when they appear on oversized fragments or chimeric fragments.

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Realigning indels—The Isaac Aligner tracks previously detected indels, over a window large enough for the current read length, and applies the known indels to all reads with mismatches.

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Generating BAM files—The first step in BAM file generation is creation of the BAM record, which contains all required information except the name of the read. The Isaac Aligner reads data from base call (BCL) files that were written during base calling on the sequencer to generate the read names. Data are then compressed into blocks of 64 kb or less to create the BAM file.