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cactus

Official home of genome aligner based upon notion of Cactus graphs

common_libs

some useful libraries for developing bioinformatic tools

edlib

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

flagger

Evaluating genome assemblies

hpp-assembly

hpp_production_workflows

WDL’s and Dockerfiles for assembly QC process

libretro-common

Reusable coding blocks useful for libretro core and frontend development, written primarily in C. Permissively licensed.

miniasm

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

research_notes

A repository for saving notes/docs for my research

secphase

Phasing reads with secondary alignments

shasta

De novo assembly from Oxford Nanopore reads.

sonlib

Small general-purpose library for C and Python with an emphasis on bioinformatics.

terra_scripts

ucscthesis

LaTeX templates for UCSC thesis and/or advancement (thesis proposal)

vg_wdl

Workflow Description Language (WDL) scripts for common vg workflows