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amptk

AMPtk: Amplicon ToolKit for NGS data (formally UFITS)

augustus

AUGUSTUS v3.2.1 for installation on Mac OS X

bac_blaster

Script to take folder of ab1 files generated from end sequencing a plasmid and map them to an assembly

bioconda-recipes

Conda recipes for the bioconda channel.

biograpy

Biological Graphic tool in Python

buscolite

BUSCOlite: simplified conserved marker gene prediction for genome annotation

complete-striped-smith-waterman-library

dockerized-genemark

Docker version of gene prediction software GeneMark

dw

dw is a docker wrapper bash script

eggnog-mapper

Fast genome-wide functional annotation through orthology assignment

evidencemodeler

source code for EVM

fac-assembly

Scripts for assembly of PE Illumina from pooled BAC/FACs

fizzy

Feature selection for biological data formats (Fizzy)

funannotate

Eukaryotic Genome Annotation Pipeline

funannotate-paper

Scripts used in funannotate manuscript

funannotate2

Eukaryotic genome annotation software.

funguild

FUNGuild: parsing OTUs into functional guilds

gag

Generates an NCBI .tbl file of annotations on a genome.

gapmm2

gapmm2: gapped alignment using minimap2 (align transcripts to genome)

gene2product

Curated list of gene names and product descriptions that pass NCBI genome submission rules.

genome_scripts

collection of random scripts for processing genome related files. the shell scripts are specific to my environment and may not work elsewhere.

gfftk

GFF toolkit

homebrew-science

:microscope: Scientific formulae for the Homebrew package manager

homebrew-tap

local homebrew tap

isonclust

De novo clustering of long transcript reads into genes

jaaws

Jon's Awesome Assembly Wrapper Script

lab_tutorial

Lab Meeting Walkthrough

laetiporus

scripts for laetiporus ms

lr-asm

Long read genome assembly scripts

medaka

Sequence correction provided by ONT Research