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
Generate GitHub-style punchcard charts with ease.
Python libraries to interact with BWA mapper
Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.
A rapid on-ramp primer for programmers who want to learn Python for doing data science research and development.
Fork of Chuck Rhode's PythonTidy script.
Convert QIIME files into Oligotyping subsets.
Quantitative Insights Into Microbial Ecology (QIIME): Official repository for software and unit tests
This is a quick and basic tutorial for R
Spatial data in R: using R as a GIS
A list of weak Bacterial assemblies in GenBank
Robot's reimagining of soups and stews
Writing reviews of academic papers
Simple R interface to forecast.io weather data
Template for DESeq2 Analysis of RNA-seq data
An R interface for PHYLIP.
transform restructuredtext documents to html5 + twitter's bootstrap css, deck.js or reveal.js
Interface to USDA Databases
This is the official development repository for samtools.
Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
Toolkit for processing sequences in FASTA/Q formats
extract 454 Genome Sequencer reads from a SFF file and convert them into a FASTQ formatted output
blast, shmlast
Genome comparison via de Bruijn graph. To get the latest stable version, please visit our site.
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.
Software Carpentry web site.
Mitochondrial Solar Plot
Lesson on using the SQL for ecology