Changes between Version 56 and Version 57 of GSoC/Ideas


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Timestamp:
03/08/12 10:44:24 (3 years ago)
Author:
gregorr
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  • GSoC/Ideas

    v56 v57  
    160160 
    161161Possible mentors: ? 
     162 
     163=== biox library (NGS, next-generation sequencing) === 
     164 
     165Orange already offers the Bioinformatics add-on but currently lacks tools for NGS (next-generation sequencing) data management and analysis. We suggest developing Python library biox (also by integrating existing state-of-the-art software) to be used in Orange. 
     166 
     167Short description of project tasks: 
     168* develop support for reading/writing/searching the most used bioinformatics file formats: fasta, fastq, bed, wig, bigWig, gtf, gff3, bedGraph. Carefully craft memory efficient representations of various features (if needed, represent features in C and connect with Python), 
     169* develop simple (programmatically easy to use) wrappers for existing NGS open source software solutions such as: read quality analysis (e.g. FASTQC), mapping of reads to reference genomes (e.g.: bowtie, bowtie2, tophat), differential expression analysis (e.g.: DESeq, baySeq), 
     170* where needed, various tools should be able to produce statistical reports in text and also graphical format (matplotlib).