Stajich Laboratory for Fungal Evolutionary Genomics

Tools

Links to Projects and Software written or contributed to by the lab.

Funannotate

Automated genome annotation pipeline that includes self-training, RNAseq incorporation in training and prediction, functional annotation, and comparative genomics. Developed by Jon Palmer with input from Jason Stajich

AAFTF

Automated Assembly For The Fungi - automated genome assembly for simple haploid genome projects

PHYling

Phylogenomic package

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BioPerl

BioPerl project code

Lab SOPs

Standard Operating Procedures for Data analyses

Zygolife LCG assembly

ZyGoLife - Low Coverage Genome assembly and annotation

Zygolife

Zygomycetes Genealoogy of Life

1000 Fungal Genomes

1kFG project

1kfg - NCBI fungi

calculating summary statistics for public fungal genomes in NCBI and downloading genomes and annotations

1kfg - 2019 Freeze

downloads and processing for 1kfg project datasets from JGI and other

1kfg - PHYling Fungi HMMs

HMMs for several public phylogenomic marker sets for Fungal Phylogenomics

FGMP

Fungal Genome Mapping Pipeline - an alternate tool for genome completeness that incorporates coding and non-coding elements

ReLocaTE2

Transposable element insertion site mapping tool using short-reads for population resequencing