Extremely accurate algorithm used to group DNA sequences from microbial communities into operational taxonomic units (proxy for species) for ecological or biomedical research. This algorithm uses t…

TextMate support for knitr

A modular pipeline for constructing Pathway/Genome Databases from environmental sequence information

A place to put docker build files

Benchmark and toy datasets

The genome annotation service provides automated gene annotation based on the RAST system. This deploys both client and service components.

NCBI Pathogen Detection Portal toolkit

Scripts to log and analyze computer usage

Profiling framework for the R language

(a) (p)erfect (c)ircle? ... tests DNA sequences for overlapping ends, then trims and rejoins, and aligns reads to test the join

Genome assembly/prediction/annotation pipeline for the Linux command line

high-throughput primer design and graphical visualization

Scaffolding Contigs Using Blat And Transcripts

Codes for Highly Pathogenic H5N1, and Swine H1 (Global and US) Clade Classifications

password script for the irssi IRC client

Normalize VCF depth for Illumina GC bias

Flux balance modeling service. Deploys both the client and service codes.

A collection of scripts to recreate historical RefSeq versions

Insert genes into genomes to aid synthetic test data generation

FAST ANNOTATION PIPELINE FOR EUKARYOTES

Search guide-RNA sequences given a genome or gene sequence

makes a mini-genome, shrinks introns, useful for developing small test sets and small data sets for workshops

Collection of scripts for generating crisprs

The m5nr is a MD5 based non-redundant sequence database that includes both protein and rRNA sequences.

Brian Muegge's old metagenomic pipeline code.

metagenomic analysis server site code

taxonomy-dependent short read 16S rRNA classifier