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03/08/12 10:44:24 (
Possible mentors: ?
=== biox library (NGS, next-generation sequencing) ===
Orange 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.
Short description of project tasks:
* 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),
* 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),
* where needed, various tools should be able to produce statistical reports in text and also graphical format (matplotlib).