Skip to content

Commit

Permalink
Updating the FASTQ entry in the NEWS file
Browse files Browse the repository at this point in the history
  • Loading branch information
peterc committed Jul 31, 2009
1 parent 82a8d7a commit bf8b255
Showing 1 changed file with 10 additions and 4 deletions.
14 changes: 10 additions & 4 deletions NEWS
Expand Up @@ -9,16 +9,22 @@ The latest news is at the top.

===================================================================

FASTQ support in Bio.SeqIO has been improved, extended and sped up since
Biopython 1.50. Support for Illumina 1.3+ style FASTQ files was added in the
1.51 beta release. Furthermore, we now follow the interpretation agreed on
the OBF mailing lists with EMBOSS and BioPerl for inter-conversion and the
valid score range for each FASTQ variant. This means Solexa FASTQ scores can
be from -5 to 62 (format name "fastq-solexa" in Bio.SeqIO), Illumina 1.3+
FASTQ files have PHRED scores from 0 to 62 (format name "fastq-illumina"),
and Sanger FASTQ files have PHRED scores from 0 to 93 (format name "fastq"
or "fastq-sanger").

Bio.Sequencing.Phd has been updated, for example to cope with missing peak
positions. The "phd" support in Bio.SeqIO has also been updated to record
the PHRED qualities (and peak positions) in the SeqRecord's per-letter
annotation. This allows conversion of PHD files into FASTQ or QUAL which may
be useful for meta-assembly.

Bio.SeqIO now observes -5 as the minimum Solexa quality score for reading
and writing Solexa FASTQ files. This is consistent with EMBOSS. Additionally,
FASTQ parsing and writing is now noticeably faster.

See the notes below for the Biopython 1.50 beta release for changes since
Biopython 1.49 was released. This includes dropping support for Python 2.3,
removing our deprecated parsing infrastructure (Martel and Bio.Mindy), and
Expand Down

0 comments on commit bf8b255

Please sign in to comment.