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- Brueffer, Christian, et al.
(författare)
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Biopython Project Update 2016
- 2016
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The Biopython Project is a long-running distributed collaborative effort, supported by the Open Bioinformatics Foundation, which develops a freely available Python library for biological computation.We present here details of the latest Biopython release - version 1.66. New features include: extended Bio.KEGG and Bio.Graphics modules to support drawing KEGG pathways with transparency; extended “abi” Bio.SeqIO parser to decode almost all documented fields used by ABIF instruments; a QCPSuperimposer module using the Quaternion Characteristic Polynomial algorithm for superimposing structures to Bio.PDB; and an extended Bio.Entrez module to implement the NCBI Entrez Citation Matching function and to support NCBI XML files with XSD schemas. Additionally we fixed miscellaneous bugs, enhanced our test suite and continued our efforts to abide by the PEP8 coding style guidelines.We are currently preparing a new release – version 1.67 – that will deprecate the ability to compare SeqRecord objects with “==”, which sometimes lead to surprising results. In addition it will feature a new experimental Bio.phenotype module for working with Phenotype Microarray data; updates to Bio.Data toinclude NCBI genetic code table 25, covering Candidate Division SR1 and Gracilibacteria; an update to Bio.Restriction to include the REBASE May 2016 restriction enzyme list; updates to BioSQL to use foreign keys with SQLite3 databases; as well as corrections to the Bio.Entrez module and the MMCIF structure parser.Our website has been migrated from MediaWiki to GitHub Pages and is now under version control. The continuous integration process on GitHub has been enhanced by including external services like Landscape, Quantified Code and Codecov to perform quality review, test coverage analysis and generation of quality metrics.Finally, our range of Docker containers has been greatly enhanced. In addition to a basic container that includes Python 2 and 3 with Biopython and all its dependencies, as well as a BioSQL container, we now also provide two versions of Jupyter notebook containers: a basic one, and a version including the Biopython tutorial as notebooks.
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| 2. |
- Brueffer, Christian, et al.
(författare)
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TopHat-Recondition : A post-processor for TopHat unmapped reads
- 2016
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Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 17:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: TopHat is a popular spliced junction mapper for RNA sequencing data, and writes files in the BAM format - the binary version of the Sequence Alignment/Map (SAM) format. BAM is the standard exchange format for aligned sequencing reads, thus correct format implementation is paramount for software interoperability and correct analysis. However, TopHat writes its unmapped reads in a way that is not compatible with other software that implements the SAM/BAM format. Results: We have developed TopHat-Recondition, a post-processor for TopHat unmapped reads that restores read information in the proper format. TopHat-Recondition thus enables downstream software to process the plethora of BAM files written by TopHat. Conclusions: TopHat-Recondition can repair unmapped read files written by TopHat and is freely available under a 2-clause BSD license on GitHub: https://github.com/cbrueffer/tophat-recondition.
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