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Sequencers use
their own output formats, and even multiple different formats per technology.
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Output formats
from Roche 454 sequencers:
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.sff is 454’s
binary(=compressed) format, including the raw data. Not the very raw images,
but flow values (flowgram), base calls, base-call qualities, read trimming
and quality.
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There are many
simple tools that “unzip” .sff into some readable textual format (see the
black example).
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.fna is a FASTA
(or FASTA-like) format including the base-called reads.
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.qual includes
qualities corresponding to bases in .fna.
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