Lab-Code-and-Hacks

This is the site where we share and update code and protocols for the Michigan Mycology Lab.

Protocols where you need mark up (images, etc.) can be added to the Wiki as new pages.

Table of Contents

Creating_NMDS_Plots

R scripts for creating NMDS plots from QIIME OTU tables

Getting_started_with_the_flux

This folder contains instuctions on how to connect to the flux as well as notes about the configuration, a list of useful unix commands, and instructions on setting up an interactive job.

MHC-Haplotype_Analyses

R scripts and example files for analysis of haplotypes

Maker_pipeline

Instructions on how to run Maker for protein prediction.

QIIME Documentation

Alisha & Alex's QIIME work

Running_Esom

Instructions and example files for running ESOM

SRA_data

Instructions on downloading SRA data to the flux

pacbio

Pacbio stuff???

phylogenetics

Instructions and example files for running raxml and mrbayes on the flux.

phylogenomics

Instructions and example files on how to pull phylogenetic markers from genomes, concatenate them, and infer a tree using the Spatafora et al. 2016 pipeline.

processing_messy_genomic_data

How to assemble and bin simple metagenomic data.

some_useful scripts

Kevin's contribution. Electric collection of scripts that may need to be re-categorized.

Loose scripts

AWS_smrt_portal_directions

[under construction]

ClusterRemover.pl

[under construction]

DataMatchingBetweenSpreadsheets

[under construction]

Fantastic_scripts_and_where_to_find_them

A list of useful scripts generated by other people and links to them

Hybrid_allele_analysis_script

[under construction]

Regular_expressions.R

Explanation of regular expressions in R

blast_quick_guide

Brief instructions on running blast locally.

connecting_to_lsa_server_on_pc

How to connect to the lsa server via pc

get_blast_accsinfo.py

[under construction]