bio-0.4.8: 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 not one, but two different, and indistinguishably so, ways to do it:

Sanger-style FastQ-format is supported with the (h)read/writeSangerQ functions, and the new IlluminaSolexa-style with (h)readwriteIllumina.

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

use Sanger-style quality information

use Illumina (>v1.3)-style quality information