Jon Palmer's repositories
funannotate
Eukaryotic Genome Annotation Pipeline
gene2product
Curated list of gene names and product descriptions that pass NCBI genome submission rules.
funannotate2
Eukaryotic genome annotation software.
dockerized-genemark
Docker version of gene prediction software GeneMark
bioconda-recipes
Conda recipes for the bioconda channel.
isONclust
De novo clustering of long transcript reads into genes
lr-asm
Long read genome assembly scripts
medaka
Sequence correction provided by ONT Research
pyspoa
Python bindings to spoa
dw
dw is a docker wrapper bash script
pipeline-umi-amplicon
Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers
eggnog-mapper
Fast genome-wide functional annotation through orthology assignment
PASApipeline
PASA software
homebrew-tap
local homebrew tap
FAC-assembly
Scripts for assembly of PE Illumina from pooled BAC/FACs
phyloma
Phylogeny using Marker-gene Analysis
funannotate-paper
Scripts used in funannotate manuscript
genome_scripts
collection of random scripts for processing genome related files. the shell scripts are specific to my environment and may not work elsewhere.
FUNGuild
FUNGuild: parsing OTUs into functional guilds
mhc_cluster
Scripts to process MHC DRB2 next-gen sequencing data
homebrew-science
:microscope: Scientific formulae for the Homebrew package manager