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O|B|F News
- Biopython 1.54 released
- The Biopython team is proud to announce Biopython 1.54, a new stable release of the Biopython library. Biopython 1.54 comes five months after our last release and brings new features, tweaks to some established functions and the usual collection of bug fixes. This is the first stable release to feature the new Bio.Phylo module which [...]
- O|B|F Google Summer of Code Accepted Students
- I?m pleased to announce the acceptance of OBF?s 2010 Google Summer of Code students, listed in alphabetical order with their project titles and primary mentors: Mark Chapman (PM Andreas Prlic) ? Improvements to BioJava including Implementation of Multiple Sequence Alignment Algorithms Jianjiong Gao (PM Peter Rose) ? BioJava Packages for Identification, Classification, and Visualization of [...]
- Illumina FASTQ files ? Read Segment Quality Control Indicator
- In another quirk to the FASTQ story, recent Illumina FASTQ files don?t actually use the full range of PHRED scores ? and a score of 2 has a special meaning, The Read Segment Quality Control Indicator (RSQCI, encoded as ?B?). Hats off to Dr Torsten Seemann for raising awareness of this issue in his post [...]
- Partial sequence files with Biopython
- This is another blog post to highlight one of the neat tricks you?ll be able to do with Biopython 1.54 (which you can help test with the Biopython 1.54 beta release). It is often useful to be able to extract a few records from a larger sequence file ? for example, some sequences of interest [...]
- Making Biopython SeqIO and AlignIO easier
- One of the small changes coming in Biopython 1.54 (which you can try out already using the Biopython 1.54 beta) is to Bio.SeqIO and Bio.AlignIO. Previously the input and output functions had required file handles, but they will now also accept filenames. This is a case of practicality beats purity (to quote the Zen of [...]
- Biopython 1.54 beta released
- A beta release for Biopython 1.54 is now available for download and testing.
- O|B|F in Google Summer of Code
- O|B|F is in Google Summer of Code, student applications due to Google April 9, 2010.
- 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. [...]
- 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 [...]
- 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 [...]
See also the latest version of the NEWS file included with each release.
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