hyphaltip

short-read-db

Database for shortreads and comparing overlap with genomic features

fungi-gene-prediction-params

Provide trained gene prediction parameters for Fungal genome annotation

Tutorial_GenomeEvolution

Genome Evolution Lecture for Phylogenomics Workshop

pan-fungal-project

A Pan-Fungal Genomes Database

GEN220_2015

GEN220 course, Fall 2015 edition

ExaML

Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI

standard-RAxML

ASTRAL

Accurate Species TRee ALgorithm

Binning

Scripts required to calculate tetramer frequencies and create input files for ESOM. See: Dick, G.J., A. Andersson, B.J. Baker, S.S. Simmons, B.C. Thomas, A.P. Yelton, and J.F. Banfield (2009). Community-wide analysis of microbial genome sequence signatures. Genome Biology, 10: R85

CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads

cocci_repeats

Coccidioides repeat analysis

Contentious_relationships_Code

Code from Shen et al Nat Eco Evo 2017

disopred

Protein structural disorder prediction

Gap2Seq

Gap2Seq is a gap filling and insertion genotyping tool.

gene2product

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

ggtree-book

:book:The ggtree book

homebrew-science

:snowflake: Scientific formulae for Homebrew and Linuxbrew (legacy)

kallisto

Near-optimal RNA-Seq quantification

Massospora_genomes

npScarf

parsnp

Personal-NGS-Cloud

PopPUNK

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

R-genomics

Lesson on data analysis and visualization in R for genomics

redundans

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

SeqPrep

Tool for stripping adaptors and/or merging paired reads with overlap into single reads.

SolidBin

A genome binning method for contig binning, based on semi-supervised spectral clustering method.

systemPipeRdata

NGS workflow templates and sample data

test_gen220_fun

VAPiD

VAPiD: Viral Annotation and Identification Pipeline