bio-0.4.7: A bioinformatics library




Support the FastQ format that combines sequence and quality. See:

Of course, this is yet another vaguely defined pseudo-standard with conflicting definitions. Of course Solexa had to go and invent a different, but indistinguishably so, way to do it:

Currently, we only support the non-Solexa FastQ, adding/subtracting 33 for the quality values.

As far as I know, FastQ is only used for nucleotide sequences, never amino acid.


Reading FastQ

parse :: [ByteString] -> Maybe (Either String (Sequence Nuc), [ByteString])Source

Parse one FastQ entry, suitable for using in unfoldr over lines from a file

Writing FastQ