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intro_python Public
Lecture Notes and Slides for UCSC CSE20, formatted as Jupyter Notebooks.
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pinchesAndCacti Public
Library for constructing pinch graphs and cactus graphs
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sonLib Public
Small general purpose library for C and Python with focus on bioinformatics.
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giraffeCapExperiments Public
Little experiments on a better mapq cap function
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ortheus Public
Evolutionary transducer based method for aligning and reconstructing indel histories
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marginAlign Public
Forked from mitenjain/nanoporeUCSC Nanopore
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cPecan Public
C + python code for pairwise multiple sequence alignment, pulling out this functionality from the Cactus alignment program.
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BME-230B Public
Forked from jvivian/BME-230BClass lectures for BME-230B
Jupyter Notebook UpdatedApr 3, 2018 -
jobTree Public
Python based pipeline management software for clusters (but checkout toil: https://github.com/BD2KGenomics/toil, its successor)
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tools for working with variation graphs
C++ MIT License UpdatedMay 4, 2017 -
signalAlign Public
Forked from ArtRand/signalAlignHMM-HDP models for MinION signal alignments
C MIT License UpdatedNov 4, 2016 -
schemas Public
Forked from ga4gh/ga4gh-schemasWork on data models and APIs for Genomic data.
Python Apache License 2.0 UpdatedNov 6, 2015 -
toil Public
Forked from DataBiosphere/toilPython 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-c…
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progressiveBenchmarks Public
Evaluation scripts for testing cactus progressive method
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matchingAndOrdering Public
Library of matching and ordering algorithms, used for "reference problem"
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RefVariationTaskTeam Public
Forked from adamnovak/RefVariationTaskTeamWork 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 me…
Apache License 2.0 UpdatedMay 13, 2014 -
referenceScripts Public
Scripts for evaluating a cactus reference genome
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assemblaScripts Public
Benchmarking scripts for assessing assemblies, used in the Assemblathon 1 project
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cactusTools Public
A home for various common but non-essential scripts for the cactus project
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