benedictpaten

intro_python

Lecture Notes and Slides for UCSC CSE20, formatted as Jupyter Notebooks.

marginAlign

UCSC Nanopore

marginPhase

sonLib

Small general purpose library for C and Python with focus on bioinformatics.

jobTree

Python based pipeline management software for clusters (but checkout toil: https://github.com/BD2KGenomics/toil, its successor)

pinchesAndCacti

Library for constructing pinch graphs and cactus graphs

cPecan

C + python code for pairwise multiple sequence alignment, pulling out this functionality from the Cactus alignment program.

pecan

Probabilistic consistency based aligner

ortheus

Evolutionary transducer based method for aligning and reconstructing indel histories

assemblaScripts

Benchmarking scripts for assessing assemblies, used in the Assemblathon 1 project

assemblaLib

Library for Assemblathon 1 analysis scripts

cactusTools

A home for various common but non-essential scripts for the cactus project

matchingAndOrdering

Library of matching and ordering algorithms, used for "reference problem"

pysqg

Prototype implementation of SQG parser in Python

Progressive-Alignment-with-Cactus

progressiveBenchmarks

Evaluation scripts for testing cactus progressive method

referenceScripts

Scripts for evaluating a cactus reference genome

toil

Python based pipeline management software for clusters that makes running recursive and dynamically scheduled computations straightforward. So far works with gridEngine, lsf, parasol and on multi-core machines.

BME-230B

Class lectures for BME-230B

giraffeCapExperiments

Little experiments on a better mapq cap function

long_read_giraffe_chainer_prototype

RefVariationTaskTeam

Work on data models and APIs for graph structures that represent the human reference genome plus common human genetic variants. Includes mapping to a reference genome, and standardization of the mechanism for referring to variants.

schemas

Work on data models and APIs for Genomic data.

signalAlign

HMM-HDP models for MinION signal alignments

vg

tools for working with variation graphs