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beroe_forskalii_mitogenome

Data related to the Beroe forskalii mitogenome manuscript.

bioawk

BWK awk modified for biological data

bioinformatics-tutorials

Tutorials on common bioinformatics skills for beginners

brizzy

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

chep

Calculate Heterozygosity with Pileup

chromsim

NA

conservfinder

cuttlery

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

cypridina.github.io

Test website for GLO

dev-notes

Development notes for bioinformatics and other things.

dpgb

dotplot + genome browser figure generator for genome assembly

emacs

Files used in customizing emacs

fast5_in_ref

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

fasta_stats

standalone fasta_stats from Meraculous

fastest_rc_python

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

genome_assembly_pipelines

A collection of snakemake scripts to streamline genome annotation

glotk

genomes of luminous organisms toolkit

gser

genome size estimation rarefaction

hdb

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

hormiphora

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

illumina_trimming_pipeline

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

ncbi_assem_summary

Generate a summary spreadsheet for genomes from NCBI.

ncbigenomes

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

nccb_website

website for Northern California Computational Biology group

odontosyllis_undecimdonta_luciferase

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

odp

oxford dot plots

pauvre

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

rbh-specs

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

yabtap

Yet another bulk transcriptome assembly pipeline