News
From Biopython
Biopython News is posted on the Open Bioinformatics Foundation shared news server. If you use news-reader software you can subscribe to Biopython news using the RDF, RSS, RSS2 or Atom feed.
O|B|F News
- Sanger FASTQ format and the Solexa/Illumina variants
- I?m delighted to announce an open access publication in Nucleic Acids Research describing the FASTQ file format based on the conventions agreed by the OBF projects: The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants Peter J. A. Cock (Biopython), Christopher J. Fields (BioPerl), Naohisa Goto (BioRuby), Michael L. Heuer (BioJava) [...]
- Biopython 1.53 released
- We are pleased to announce the availability of Biopython 1.53, a new stable release of the Biopython library, three months after the release of Biopython 1.52. This is our first release since migrating from CVS to git for source code control. There have been some additions to our core objects ? the Seq (and related UnknownSeq) [...]
- Interleaving paired FASTQ files with Biopython
- This post is about paired end data (FASTA or FASTQ) and manipulating it with Biopython?s Bio.SeqIO module (see also FASTQ conversions & speeding up FASTQ). There are two main ways of presenting paired end data in FASTA or FASTQ files: Paired files, with matching entries for the forward and reverse reads (probably the norm with Illumina data) Single [...]
- Working with FASTQ files in Biopython when speed matters
- Biopython's SeqIO interface revolves around SeqRecord objects which can impose a speed penalty. For FASTQ files the quality string gets turned into a list of integers on parsing, and then re-encoded back to ASCII on writing. Working directly with the raw strings is less flexible, but much faster.
- Biopython CVS to git migration
- Biopython has now moved from CVS to a , hosted on who kindly provide git hosting for open source projects free of charge. The have been for some time, so we are in good company.
- Biopython 1.52 released
- We are pleased to announce the availability of Biopython 1.52, a new stable release of the Biopython library. It may only have been one month since the last release, but in that time we?ve added enough useful features to warrant a new release. In particular, Biopython 1.52 includes more substantial support for population genetics, and adds [...]
- Simpler, optimized format conversion with Biopython
- In this post we'll look at the new function that both and will get in Biopython 1.52. This allows easier file conversion, and internally provides a mechanism for specific optimisations, such as for FASTQ conversions.
- Indexing sequence files with Biopython
- The forthcoming release of 1.52 will include a couple of nice improvements to the , and here we're going to introduce the new function.
- Biopython 1.51 released
- We are pleased to announce the release of Biopython 1.51.This new stable release enhances version 1.50 (released in April) by extending the functionality of existing modules, adding a set of application wrappers for popular alignment programs and fixing a number of minor bugs. In particular, the SeqIO module can now write Genbank files [...]
- Biopython 1.51 beta released
- A beta release for Biopython 1.51 is now available for download and testing. In the two months since Biopython 1.50 was released, we have introduced support for writing features in GenBank files using Bio.SeqIO, extended SeqIO?s support for the FASTQ format to include files created by Illumina 1.3+, and added a new set of application wrappers [...]
See also the latest version of the NEWS file included with each release.
P.S. You can also follow us on twitter!
