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multigwas

MultiGWAS: A tool for GWAS analysis on tetraploid organisms by integrating results of four GWAS software

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

nanopolish

Signal-level algorithms for MinION data

novograph

NovoGraph: building whole genome graphs from long-read-based de novo assemblies

phyling_unified

Unified PHYling pipeline for species tree building from annotated genomes (see https://github.com/stajichlab/AAFTF and https://github.com/nextgenusfs/funannotate for assembly and annotation steps)

pilon

Pilon is an automated genome assembly improvement and variant detection tool

polyploid-genotyping

SNP genotyping in polyploids

qtl-seq

QTL-seq pipeline to identify causative mutations responsible for a phenotype

qtlseqr

QTLseqr is an R package for QTL mapping using NGS Bulk Segregant Analysis

rnabio.org

website for the rnaseq course

rnaseq-nf

RNASeq-NF is an NGS analysis pipeline for RNA expression quantification.

rnaseqview

RNA-seq Viewer Team at the NCBI-assisted Boston Genomics Hackathon

scripts

Scripts for analysis used during the course

snp-sites

Finds SNP sites from a multi-FASTA alignment file

ssake

🍶Genome assembly with short sequence reads

star_protocols_wes3x

Functional code templates for the Star Protocols paper describing consolidated WES variant calling with 3 callers

sweep

Sliding Window Extraction of Explicit Polymorphisms

tassel-workshop

This site contains sample files and instructions for the TASSEL workshop hosted by the UMN Plant Breeding Center.

tetraploidsnpmap

utilities

A bunch of scripts for bioinformatic purposes

vcf2msa.py

Package for writing multiple sequence alignments of pseudo-references from a VCF file with a reference genome

vcfr_documentation

Documentation for vcfR

virusdiscoveryproject

Software, architecture, and data index design for the 2018/2019 Virus Discovery Project

xftools

Tools developed for use in Xiaoqi Feng's lab.

zevrtricks

Next Gen Seq and Plotting