Barrick Lab

breseq

breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R.

LTEE-Ecoli

Genomics resources for the Long-Term Evolution Experiment with E. coli

ostir

Software for predicting translation initiation rates in bacteria

pLannotate

Webserver and command line tool for annotating engineered plasmids

breseq-gui

Electron GUI for breseq

brnaseq

Basic analysis of bacterial RNAseq data for differential gene expression

efm-calculator

Evolutionary Failure Mode Calculator

barricklab

General data analysis spreadsheets and scripts

cryptkeeper

Tool for visualizing unintentional bacterial gene expression from a DNA sequence

fitnessR

R package for calculating relative fitness from co-culture competition assays

igem2020

University of Texas at Austin 2020 iGEM Team

mAdCap-Seq

Scripts to analyze multiplex adaptome sequencing data

nsAA-kit

Scripts for nsAA measurement kit

promoter-calculator

brefito

Snakemake pipelines for assembling and annotating bacterial reference sequences

Abaylyi-EE

Acinetobacter baylyi ADP1 evolution and engineering

bioconda-recipes

Conda recipes for the bioconda channel.

breseq-ext-cnv

breseq copy number variation extension

breseq-ext-paired-end

breseq extension for calling mutations from paired end read mapping

FragGeneScan

FUGUES

Protocols for Functional Genomics using Engineered Symbionts (FUGUES)

genomediff-python

GenomeDiff (*.gd) file parser for Python

igem2019

Scripts and datasets for measuring BioBrick plasmid burden.

igem2021

LTEE-metagenomic

Time-resolved metagenomic sequencing of Lenski's long-term evolution experiment with Escherichia coli

ND-Bartonella-EE

Code for analyzing mutations that evolved in Bartonella bacteria passaged through rodents in the laboratory.

ND-Bartonella-SSR

RhoTermPredict

teachPress

Fork of teachPress (course and publication management plugin for WordPress) with some customizations

widespread-recurrent-part-variants

Analysis code for identifying genetic part variants in engineered plasmids