JackieGOO's repositories
bioinformaticsclass_SAGseembly
Assemble a SAG for ENVS6492
dada2
Accurate sample inference from amplicon data with single nucleotide resolution
BioData
All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
AMRocks
Scripts used for Atlantis Massif crustal and sediment microbial analysis
Anvio
Using Anvio on the Bigelow Server
AssemblyMetagenome
Q control and Assembly of metagenomic reads for Atlantis Massif seq
bin-checkm
bin via metabat + checkM: Bigelow Specific
pavian
🌈 Interactive analysis of metagenomics data
seaicespiral
Sea Ice Death Spiral animation
dna-profiling
DNA Analysis
canu
A single molecule sequence assembler for genomes large and small.
mothur
Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Immunology at The University of Michigan. This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
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
markdown-here
Google Chrome, Firefox, and Thunderbird extension that lets you write email in Markdown and render it before sending.
vsearch
Versatile open-source tool for metagenomics
blobology
Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step
datasharing
The Leek group guide to data sharing