Discover @benedictpaten Open Source projects

Benedict Paten (@benedictpaten)

benedictpaten

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Global Rank 100,504 (Top 4 %)
Followers 134
Following 15
Registered over 13 years ago
Most used languages

C
62.5 %

Python
18.8 %

TeX
6.3 %

Java
6.3 %

Jupyter Notebook
6.3 %
Location 🇺🇸 United States
Country Total Rank 24,596
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Jupyter Notebook
1,904

C
2,111

TeX
6,357

intro_python

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

Jupyter Notebook

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

pecan

Probabilistic consistency based aligner

cPecan

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

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

pysqg

Prototype implementation of SQG parser in Python

matchingAndOrdering

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

Progressive-Alignment-with-Cactus

referenceScripts

Scripts for evaluating a cactus reference genome

progressiveBenchmarks

Evaluation scripts for testing cactus progressive method