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Collection of useful code related to biological analysis. Much of this isdiscussed with examples atBlue collar bioinformatics.

All code, images and documents in this repository are freely available for alluses. Code is available under theMIT licenseand images, documentations and talks under theCreative Commons No RightsReserved (CC0) license.

Some projects which may be especially interesting:

• CloudBioLinux -- An automated environment to install useful biological software andlibraries. This is used to bootstrap blank machines, such as those you'dfind on Cloud providers like Amazon, to ready to go analysis workstations.See theCloudBioLinux effort for more details. This projectmoved to its own repository athttps://github.com/chapmanb/cloudbiolinux.
• gff -- A GFF parsing library in Python, aimed for inclusion into Biopython.
• nextgen -- A python toolkit providing best-practice pipelines for fullyautomated high throughput sequencing analysis. This project hasmoved into its own repository:https://github.com/chapmanb/bcbio-nextgen
• distblast -- A distributed BLAST analysis running for identifying best hits ina wide variety of organisms for downstream phylogenetic analyses. The codeis generalized to run on local multi-processor and distributed Hadoopclusters.