breseq

breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for haploid microbial-sized genomes. breseq is a command line tool implemented in C++ and R. It will compile and function on a variety of Unix platforms, including MacOSX and Cygwin. It reports single-nucleotide mutations, point insertions and deletions, large deletions, and new junctions supported by mosaic reads (such as those produced by new mobile element insertions) in an annotated HTML format.

Learn more	Online breseq documentation

Download	Latest version from GitHub

Comprehensive Analysis of Mutations in Evolved Microbes Using breseq

ASM Microbe 2021 On-Demand Workshop (June 20-24)
Introduction: Identifying Mutations and Studying Microbial Genome Evolution with breseq

Watch Video Download Slides

Antibiotic Resistance Reversal: breseq Analysis of Experimental Evolution, Compared with FACS Competition Assays of Relative Fitness
Joan Slonczewski
Kenyon College

Identifying Adaptive Paths in Host-Plasmid Coevolution Using breseq
Olivia Kosterlitz
University of Washington

Code and directions for making genome plots

Decoding Evolution-In-Action in Classroom Experiments That Simulate Infection Biology Using breseq
Vaughn Cooper
University of Pittsburgh

EvolvingSTEM program website

ALEdb: A Living High-Quality Database of Mutations from Adaptive Evolution Experiments Powered by breseq
Adam Feist
University of California, San Diego

Visit the Adaptive Laboratory Evolution Database (ALEdb)

Zoom Workshop: Advanced Topics (July 22, 2021)

Watch Recording

Download Slides

Download Examples

Zoom Workshop: Introductory Topics (July 20, 2021)

Watch Recording

Download Slides

Example 1a: Analyzing an evolved E. coli clone with a high quality reference sequence for its ancestor (LTEE Ara+1 50,000 generations, Clone A)
breseq -l 80 -r REL606.gbk SRR2584524.fastq.gz
View Results

Example 1b: What the results look like if you run this same clonal sample in polymorphism mode (LTEE Ara+1 50,000 generations, Clone A)
breseq -p -l 80 -r REL606.gbk SRR2584524.fastq.gz
View Results

Example 2: Results for another evolved clone that was sequenced with longer reads (LTEE Ara+1 50,000 generations, Clone B)
breseq -r REL606.gbk SRR2584534_1.fastq.gz SRR2584534_2.fastq.gz
View Results

Example 3: Analyzing the mixed population that both of these clones were isolated from (LTEE Ara+1 50,000 generations, Population)
breseq -j 8 -p -r REL606.gbk SRR6173952_1.fastq.gz SRR6173952_2.fastq.gz
View Results

Example 4: Results from mapping to reference genome of a closely related strain–many predictions (links removed to save disk space).
breseq -r NC_000913.3.MG1655.gbk SRR2584534_1.fastq.gz SRR2584534_2.fastq.gz
View Results

Example 5: Analyzing an E. coli cell that contains a plasmid
breseq -r E._coli_W3110_NC_007779.1.gbk -r GFP_Plasmid_SKO4.gbk AR_E1_GTTTCG_L005_R2_001.fastq.gz AR_E1_GTTTCG_L005_R1_001_1.fastq.gz AR_E1_GTTTCG_L005_R1_001.fastq.gz AR_E1_GTTTCG_L005_R2_001_1.fastq.gz
View Results

Example 6a: Locating the insertion site of an integration cassette in the A. baylyi genome using a junction reference (best option)
breseq --junction-only-reference pBTK622_tdk-kanR_cassette_for_Golden_Transformation.gbk -r Acinetobacter-baylyi-ADP1-WT.gff3 G2_CCGTCC_L007_R1_001.fastq.gz G2_CCGTCC_L007_R2_001.fastq.gz
View Results

Example 6b: Same sample not using junction reference
breseq -r pBTK622_tdk-kanR_cassette_for_Golden_Transformation.gbk -r Acinetobacter-baylyi-ADP1-WT.gff3 G2_CCGTCC_L007_R1_001.fastq.gz G2_CCGTCC_L007_R2_001.fastq.gz
View Results

Example 6c: Same sample using targeted mode
breseq -t -r pBTK622_tdk-kanR_cassette_for_Golden_Transformation.gbk -r Acinetobacter-baylyi-ADP1-WT.gff3 G2_CCGTCC_L007_R1_001.fastq.gz G2_CCGTCC_L007_R2_001.fastq.gz
View Results

Example 7a: Mapping to a de novo assembled reference
breseq -r assembly.fasta SRR2584534_1.fastq.gz SRR2584534_2.fastq.gz
View Results

Example 7b: Mapping to a de novo assembled reference using contig mode (best option)
breseq -c assembly.fasta SRR2584534_1.fastq.gz SRR2584534_2.fastq.gz
View Results

Feedback and Bug Reporting

Please report bugs on GitHub.

Tutorial input and results files for breseq book chapter

Deatherage, D.E., Barrick, J.E.. (2014) Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol. Biol. 1151:165-188. «PubMed»

Download Link	Size	Description
Clonal_Sample.tgz	267M	Input files for clonal sample
Clonal_Output.tgz	1.2M	Output files for clonal sample
Population_Sample.tgz	1.4G	Input files for time-course of population samples
Population_Output.tgz	11M	Output files for time-course of population samples, including comparison
Mutation_Examples.tgz	199K	Examples of using unassigned evidence to predict complex mutations
Poor_Evidence_Examples.tgz	139K	Example output showing characteristics of poor evidence

Other Resources

Previous Versions:

Previous versions from 0.24rc6 to 0.25d (barricklab.org)

Previous versions up to 0.24rc6 (Google Code)

Additional test data and an example of breseq output:

FASTQ reads for E. coli strain REL8593A (200M)

Reference genome (REL606)

Example of breseq output