Josh Herr's repositories
alignerviz
A simple tool to visualize sequences using Vlachos et al's technique
arcdiagram
R package arcdiagram
BGI-data-analysis
assemblies, annotations, further analysis on sequenced strains from the EHEC outbreak
CONTIGuator
Bacterial genomes finishing tool for structural insights on draft genomes
its-reference-otus
A reference set of ITS OTUs derived from UNITE for use with QIIME
jekyll_template
a simple jeckyll template
MetaVelvet
An extension of Velvet assembler to de novo metagenome assembly from short sequence reads
mobedac-fungi
MOBeDAC Fungi Database
PythonTidy
Fork of Chuck Rhode's PythonTidy script.
SimSeq
An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries . Additionally the program provides the ability to model both site and base specific error, and scripts are provided to train this error model on real datasets. My hope in creating this program is to generate as realistic data as possible to assist in assessing the accuracy of genome assembly tools.
TAXAassign
Pipeline to annotate sequences at different taxonomic levels using NCBI's taxonomy
Topiary-Explorer
Interactive phylogenetic tree viewing software
toy_bottle_bootstrap_app
A demonstration of using bottle with bootstrap for basic web app development