Pinned Repositories
alignment_visualization
Visualize how reads align to a reference
cartpole_policy_gradient
a simple 1st order PG solution to the openAI cart pole problem (adapted from @ts1839) and an RNN based PG variation on this
GFAse
Tool for globally phasing diploid assembly graphs with orthogonal data
nanopore_assembly_and_polishing_assessment
Automation of pipelines that depend on preexisting assembly, polishing, and alignment tools. Performance evaluation and visualization of assembly and polishing
runlength_analysis
for analyzing sequence data in RLE space
shallow_neural_network_example
A jupyter notebook demonstrating the application of a simple neural network to approximation of a region of the sine function
shasta
Experimental software for de novo assembly from Nanopore sequencing data.
simple-dotplot
Very simple and configurable all-in-one dotplot program
TaskManager
Monitors resources and sends notifications, ideal for managing large computational experiments on AWS
GetBlunted
For bluntifying overlapped GFAs
rlorigro's Repositories
rlorigro/GFAse
Tool for globally phasing diploid assembly graphs with orthogonal data
rlorigro/nanopore_assembly_and_polishing_assessment
Automation of pipelines that depend on preexisting assembly, polishing, and alignment tools. Performance evaluation and visualization of assembly and polishing
rlorigro/simple-dotplot
Very simple and configurable all-in-one dotplot program
rlorigro/TaskManager
Monitors resources and sends notifications, ideal for managing large computational experiments on AWS
rlorigro/shasta
Experimental software for de novo assembly from Nanopore sequencing data.
rlorigro/FlavorDetector
Where is the indian food at all times
rlorigro/great_lengths
Very simple tool for generating read length distributions from fastq/fasta files
rlorigro/Liger2LiGer
Nanopore chimera splitting/detection tool
rlorigro/runlength_analysis_cpp
Building runlength frequency matrices for sequence data
rlorigro/sv_align
Experimental methods for finding SVs in a GFA
rlorigro/sv_merge
C++ implementation of rlorigro/hapslap
rlorigro/dbg_compare
rlorigro/dbg_compare_wdl
rlorigro/dipcall_asm10
Reference-based variant calling pipeline for a pair of phased haplotype assemblies
rlorigro/GraphAligner
rlorigro/hapslap
rlorigro/jackalope
rlorigro/jungle_gym
rlorigro/libbdsg
Optimized sequence graph implementations for graph genomics
rlorigro/libvgio
A dynamic library that provides io for the vg toolkit.
rlorigro/multiobjective_optimization
A simple demo showing the use of the distance metric to minimize multiple objectives
rlorigro/mungus
A screenshot aligner that stitches images as you walk through a 2d game
rlorigro/overlap_analysis
rlorigro/quast
Genome assembly evaluation tool
rlorigro/receptor_detector
Solution to sequence labeling problem
rlorigro/rlorigro.github.io
Personal website for Ryan LR
rlorigro/sdsl-lite
Succinct Data Structure Library 2.0
rlorigro/ucscthesis
LaTeX templates for UCSC thesis and/or advancement (thesis proposal)
rlorigro/vg
tools for working with genome variation graphs
rlorigro/WFA2-lib
WFA-lib: Wavefront alignment algorithm library v2