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centromere_seeker

bash script to search for centromeric repeat patterns in PacBio data, using several current tools (trf and R)

custom-repeat-library

Code for the Custom Repeat Library protocol as described: http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction-Advanced

fcs

Foreign Contamination Screening caller scripts and documentation

go_kegg_annotation

GO KEGG annotation

jellyfish-infer-genome-size

nanocaller

Variant calling tool for long-read sequencing data

pcap-gwas

Relevant scripts for manuscript: 'Genome-wide association study in New York Phytophthora capsici isolates reveals loci involved in mating type and mefenoxam sensitivity'

planets

polygonia_calbum_genomics

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

rnaseq_workshop

This repository contains a walkthrough of how to analyze RNA-Seq data, using a sample dataset from Bernal et al. 2020 (Science Advances). This repository will be used in the RNA-Seq data analysis workshop held at UT Chattanooga from August 10-12, 2022.

sv-benchmark

Public Benchmark of Long-Read Structural Variant Caller on PacBio CCS HG002 Data

sv_gwas

This repository contains the code used for SV-GWAS project