Pinned Repositories
cPecan
C + python code for pairwise multiple sequence alignment, pulling out this functionality from the Cactus alignment program.
intro_python
Lecture Notes and Slides for UCSC CSE20, formatted as Jupyter Notebooks.
jobTree
Python based pipeline management software for clusters (but checkout toil: https://github.com/BD2KGenomics/toil, its successor)
marginAlign
UCSC Nanopore
marginPhase
pinchesAndCacti
Library for constructing pinch graphs and cactus graphs
sonLib
Small general purpose library for C and Python with focus on bioinformatics.
cactus
Official home of genome aligner based upon notion of Cactus graphs
toil
A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.
vg
tools for working with genome variation graphs
benedictpaten's Repositories
benedictpaten/intro_python
Lecture Notes and Slides for UCSC CSE20, formatted as Jupyter Notebooks.
benedictpaten/marginAlign
UCSC Nanopore
benedictpaten/marginPhase
benedictpaten/sonLib
Small general purpose library for C and Python with focus on bioinformatics.
benedictpaten/jobTree
Python based pipeline management software for clusters (but checkout toil: https://github.com/BD2KGenomics/toil, its successor)
benedictpaten/pinchesAndCacti
Library for constructing pinch graphs and cactus graphs
benedictpaten/cPecan
C + python code for pairwise multiple sequence alignment, pulling out this functionality from the Cactus alignment program.
benedictpaten/pecan
Probabilistic consistency based aligner
benedictpaten/ortheus
Evolutionary transducer based method for aligning and reconstructing indel histories
benedictpaten/assemblaScripts
Benchmarking scripts for assessing assemblies, used in the Assemblathon 1 project
benedictpaten/assemblaLib
Library for Assemblathon 1 analysis scripts
benedictpaten/cactusTools
A home for various common but non-essential scripts for the cactus project
benedictpaten/matchingAndOrdering
Library of matching and ordering algorithms, used for "reference problem"
benedictpaten/pysqg
Prototype implementation of SQG parser in Python
benedictpaten/Progressive-Alignment-with-Cactus
benedictpaten/progressiveBenchmarks
Evaluation scripts for testing cactus progressive method
benedictpaten/referenceScripts
Scripts for evaluating a cactus reference genome
benedictpaten/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.
benedictpaten/BME-230B
Class lectures for BME-230B
benedictpaten/giraffeCapExperiments
Little experiments on a better mapq cap function
benedictpaten/long_read_giraffe_chainer_prototype
benedictpaten/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.
benedictpaten/schemas
Work on data models and APIs for Genomic data.
benedictpaten/signalAlign
HMM-HDP models for MinION signal alignments
benedictpaten/vg
tools for working with variation graphs