nextgenusfs

funannotate

Eukaryotic Genome Annotation Pipeline

amptk

AMPtk: Amplicon ToolKit for NGS data (formally UFITS)

redmask

Genome assembly soft-masking using Red (REpeat Detector)

augustus

AUGUSTUS v3.2.1 for installation on Mac OS X

genome_scripts

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

gene2product

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

gfftk

GFF toolkit

buscolite

BUSCOlite: simplified conserved marker gene prediction for genome annotation

funannotate2

Eukaryotic genome annotation software.

gapmm2

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

funannotate-paper

Scripts used in funannotate manuscript

jaaws

Jon's Awesome Assembly Wrapper Script

mhc_cluster

Scripts to process MHC DRB2 next-gen sequencing data

phyloma

Phylogeny using Marker-gene Analysis

bioconda-recipes

Conda recipes for the bioconda channel.

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

FAC-assembly

Scripts for assembly of PE Illumina from pooled BAC/FACs

FUNGuild

FUNGuild: parsing OTUs into functional guilds

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

lr-asm

Long read genome assembly scripts

medaka

Sequence correction provided by ONT Research

nextgenusfs.github.io

notebooks

PASApipeline

PASA software

pipeline-umi-amplicon

Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers

pyspoa

Python bindings to spoa