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Achievement: Starstruckx2Achievement: Arctic Code Vault ContributorAchievement: Pull Shark

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  • odp Public

    oxford dot plots

    Python 147 10 GNU General Public License v3.0 Updated Mar 5, 2025

  • genome_assembly_pipelines Public

    A collection of snakemake scripts to streamline genome annotation

    Python 9 1 GNU General Public License v3.0 Updated Feb 27, 2025

  • genome_reviews Public

    public reviews for genome assemblies

    Updated Feb 16, 2025

  • pauvre Public

    Pauvre: QC and genome browser plotting Oxford Nanopore and PacBio long reads.

    C 53 13 Updated Nov 9, 2024

  • chromsim Public

    NA

    Python 1 GNU General Public License v3.0 Updated Aug 1, 2024

  • ConservFinder Public

    Forked from Nepomorpha/ConservFinder
    Python Updated Apr 19, 2024

  • rbh-specs Public

    specifications for the rbh file formats used by the odp software.

    Updated Apr 15, 2024

  • Illumina_trimming_pipeline Public

    This pipeline trims HiSeq shotgun, Dovetail Chicago, and HiC data.

    Python Updated Apr 6, 2024

  • nccb_website Public

    website for Northern California Computational Biology group

    HTML 2 Apache License 2.0 Updated Mar 19, 2024

  • ncbigenomes Public

    A script that QCs and plots how many chromosome-scale genomes are on NCBI

    Python GNU General Public License v3.0 Updated Mar 15, 2024

  • cypridina.github.io Public

    Test website for GLO

    SCSS MIT License Updated Jan 30, 2024

  • gser Public

    genome size estimation rarefaction

    Makefile 1 MIT License Updated Jan 3, 2023

  • DPGB Public

    dotplot + genome browser figure generator for genome assembly

    Python Updated Feb 1, 2021

  • yabtap Public

    Yet another bulk transcriptome assembly pipeline

    Python 1 Updated Jan 24, 2021

  • chep Public

    Calculate Heterozygosity with Pileup

    Python 6 Updated Dec 17, 2020

  • hdb Public

    Het De Bruijn graph - for finding heterozygous genome regions in k-mer space.

    C++ 1 Updated Dec 15, 2020

  • hormiphora Public

    Hormiphora californensis genome annotation and supplemental materials related to the genome assembly.

    annotation genomics hi-c pacbio pacbio-data ctenophora
    HTML 1 Updated Oct 9, 2020

  • brizzy Public

    A program to easily take spectra with Ocean Optics spectrometers. It's a breeze to use.

    Python 4 2 Updated Oct 7, 2020

  • fasta_stats Public

    standalone fasta_stats from Meraculous

    C++ 4 Other Updated Sep 15, 2020

  • NCBI_assem_summary Public

    Generate a summary spreadsheet for genomes from NCBI.

    C++ Other Updated Jun 18, 2020

  • Bioinformatics-tutorials Public

    Tutorials on common bioinformatics skills for beginners

    1 Updated Oct 24, 2019

  • beroe_forskalii_mitogenome Public

    Data related to the Beroe forskalii mitogenome manuscript.

    HTML 1 Updated Sep 17, 2019

  • cuttlery Public

    CUTTlery: Codon Usage Table Tools and Bayesian determination of ORF protein coding-ness.

    Python 5 Updated May 17, 2019

  • dev-notes Public

    Development notes for bioinformatics and other things.

    Updated Oct 9, 2018

  • odontosyllis_undecimdonta_luciferase Public

    This repository contains analyses required to recreate the analyses found in Schultz, Kotlobay, et al. 2018

    HTML Updated May 26, 2018

  • fastest_rc_python Public

    what is the fastest way to get the reverse complement of a DNA string in python

    Python 2 1 Updated Apr 6, 2018

  • fast5_in_ref Public

    Forked from mbhall88/fast5seek

    Subset of fast5 files contained in a fastq, BAM, or SAM file.

    Python MIT License Updated Jan 13, 2018

  • bioawk Public

    Forked from lh3/bioawk

    BWK awk modified for biological data

    C Updated Oct 18, 2017

  • gloTK Public

    genomes of luminous organisms toolkit

    Python 4 GNU General Public License v3.0 Updated May 4, 2017

  • emacs Public

    Files used in customizing emacs

    Emacs Lisp Updated Apr 12, 2016