Name: Josh Herr
Type: User
Company: University of Nebraska
Bio: I am an Assistant Professor at the University of Nebraska. I study the genomics and metagenomics of plant-microbe interactions with a focus on mycology.
Location: Lincoln, NE, USA
Blog: http://joshuaherr.com
Josh Herr's Projects
The quickest way to start and publish your Jekyll powered blog. 100% compatible with GitHub pages.
Jekyll + lunr.js = static websites with powerful full-text search using JavaScript
a simple jeckyll template
A jQuery plugin to build a website on the infinite canvas
Open Notebook
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
Tools to evaluate the diversity of metagenomics sample
Lesson on Getting to Know Your Data for genomics
Kraken taxonomic sequence classification system
Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/).
This is the website of my research laboratory
LaTeX classes for formatting scientific documents, including US federal grant proposals.
A small library for dealing with .crispr files
A short tutorial on how to run local BLAST.
An example of a data analysis pipeline using Make
A metagenomic and isolate genome assembly pipeline built with AMOS
An extension of Velvet assembler to de novo metagenome assembly from short sequence reads
A framework built using Meteor.
My Working Microbial Genome Assembly & Annotation Pipeline
Mining CRISPRs in Environmental Datasets
MIX: Combining multiple assemblies from NGS data
Scan contig files against PubMLST typing schemes
MOBeDAC Fungi Database
Repository to create and maintain an Amazon AMI for mothur
Various scripts and recipes for working with nanopore data
Open Lab Notebook
Exploring microbial patterns through subtle nucleotide variation within 16S rRNA gene tag sequences of closely related taxa
Useful bash one-liners for bioinformatics.
POPBAM: Tools for Evolutionary Analysis of Short Read Sequence Alignments
A tool for bacterial gene assembly.