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ABOUT BIO::SEQREADER

Bio::SeqReader provides developers simple-to-use classes for reading sequence
data in standard formats. This currently includes FASTA and FASTQ.

Bio::SeqReader::Fasta. The FASTA (Pearson) sequence format is described in the
documentation associated with the FASTA suite as introduced in W. R. Pearson
and D. J. Lipman. (1988) "Improved tools for biological sequence comparison,"
Proceedings of the National Academy of Sciences USA 85. See for example
http://fasta.bioch.virginia.edu/fasta_www2/fasta_guide.pdf or
http://en.wikipedia.org/wiki/FASTA_format. The original format allows for the
use of a semicolon (";") to introduce the sequence header. Bio::SeqReader::Fasta
will handle this correctly.

Bio::SeqReader::Fastq. The FASTQ format is described formally in P. J. A. Cock,
C. J. Fields, N. Goto, M. L. Heuer, P. M. Rice. (2010) "The Sanger FASTQ file
format for sequences with quality scores, and the Solexa/Illumna FASTQ
variants," Nucleic Acids Research 38. Note that it specifically allows for
multiline sequence and quality score information, and Bio::SeqReader::Fastq is
designed to handle this correctly.

INSTALLATION

To install this module first create the Makefile from Makefile.PL by running

  perl Makefile.PL

or for a nonstandard location (you'll probably need to adjust PERL5LIB later)

  perl Makefile.PL INSTALL_BASE=/path/to/my/perlmods

or

  perl Makefile.PL PREFIX=/path/to/my/perllibs

Then

  make
  make test
  make install

DEPENDENCIES

Bio::SeqReader requires only core Perl.

COPYRIGHT AND LICENSE

This library is free software; you can redistribute it and/or modify it under
the same terms as Perl itself, either Perl version 5.10.0 or, at your option,
any later version of Perl 5 you may have available.

Copyright (C) 2012, John A. Crow
Copyright (C) 2012, National Center for Genome Resources




