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  • svmu Public

    A program to call variants from genome alignment

    C++ 75 18 GNU General Public License v3.0 Updated Mar 18, 2024

  • quickmerge Public

    A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.

    C++ 198 31 GNU General Public License v3.0 Updated Nov 18, 2022

  • dspr-asm Public

    Contains scripts and programs used to generate assemblies and variants for the DSPR project

    R 8 4 GNU General Public License v3.0 Updated May 13, 2021

  • butterfly-genomesize Public

    Contains scripts for analysis and figures of the butterfly genome size manuscript

    GNU General Public License v3.0 Updated Mar 3, 2021

  • sim-complex Public

    Contains assemblies and scripts relevant to the sim-complex paper

    GNU General Public License v3.0 Updated Dec 17, 2020

  • stephensi_genome Public

    Contains scripts and detailed methods used for making figures and data analysis

    1 Updated Aug 1, 2020

  • dedup Public

    Separates redundant contigs from an assembly

    C++ GNU General Public License v3.0 Updated Jan 14, 2020

  • diploid-asm Public

    Contains prototype scripts for diploid assembly of long reads

    C++ 1 GNU General Public License v3.0 Updated Jan 9, 2020

  • mlift Public

    A mummer based genomic coordinate liftover tool

    C++ 8 2 GNU General Public License v3.0 Updated Nov 7, 2019

  • dspr-popgen Public

    Contains programs and scripts for the dspr popgen project

    C++ GNU General Public License v3.0 Updated Jul 6, 2019

  • mito-finder Public

    Assembling mitochondrial genomes from long molecule sequences

    5 1 GNU General Public License v3.0 Updated Jul 3, 2019

  • mscaffolder Public

    A comparative genome scaffolding tool

    C++ 17 5 GNU General Public License v3.0 Updated Oct 6, 2018

  • mplotter Public

    Creates publication quality dot plot using ggplot

    C++ 9 3 GNU General Public License v3.0 Updated Oct 3, 2018

  • Assembly-utils Public

    Some useful programs for genome assemblies with long molecules

    C++ 1 GNU General Public License v3.0 Updated Dec 1, 2017

  • emersonlab.github.io Public

    Forked from EmersonLab/emersonlab.github.io

    Website for the Emerson Lab at UCI

    HTML Updated Aug 24, 2017

  • Assembly-error Public

    Methods and notes on how to detect assembly errors in long molecule based assemblies

    1 GNU General Public License v3.0 Updated Jun 17, 2017

  • proberead Public

    A light weight utility program to extract reads that span genomic intervals

    C++ 2 1 GNU General Public License v3.0 Updated Jun 1, 2017

  • FALCON_unzip Public

    Forked from PacificBiosciences/FALCON_unzip

    Making diploid assembly becomes common practice for genomic study

    Python BSD 3-Clause Clear License Updated Dec 21, 2016

  • molevol-utils Public

    Simple utilities for molecular evolution etc.

    C++ GNU General Public License v3.0 Updated Nov 23, 2015