(r59) ToolsBacterialGenomeResequencing < Lab

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---+ <b><i>breseq</i></b>
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__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 <nop>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.

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| *Learn more* | %ICON{viewtopic}% [[%ATTACHURL%/documentation][Online __breseq__ documentation]] |

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| *Download* | %ICON{download}% [[https://github.com/barricklab/breseq/releases/latest][Latest version from GitHub]] |

---++ Comprehensive Analysis of Mutations in Evolved Microbes Using _breseq_
*ASM Microbe 2021 On-Demand Workshop (June 20-24)* %BR%
Introduction: Identifying Mutations and Studying Microbial Genome Evolution with breseq %BR% 
<a href="https://utexas.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78b03d53-a98f-4f4c-8343-ad6a01540017"> %ATTACHURL%/ASM_Recording_Poster.png </a>

%ICON{mov}% [[https://utexas.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78b03d53-a98f-4f4c-8343-ad6a01540017][ Watch Video]] %ICON{pdf}% [[%ATTACHURL%/ASM_Microbe_2021_slides_Barrick.pdf][Download Slides]]

Antibiotic Resistance Reversal: _breseq_ Analysis of Experimental Evolution, Compared with FACS Competition Assays of Relative Fitness %BR%
*Joan Slonczewski* %BR%
_Kenyon College_

Identifying Adaptive Paths in Host-Plasmid Coevolution Using _breseq_ %BR%
*Olivia Kosterlitz* %BR%
_University of Washington_

%ICON{code}% [[https://github.com/livkosterlitz/Breseq_genome_plots][Code and directions for making genome plots]]

Decoding Evolution-In-Action in Classroom Experiments That Simulate Infection Biology Using _breseq_  %BR%
*Vaughn Cooper* %BR%
_University of Pittsburgh_

<img src="%ATTACHURL%/evolvingstem.png">

%ICON{external}% [[https://evolvingstem.org/][EvolvingSTEM program website]]

ALEdb: A Living High-Quality Database of Mutations from Adaptive Evolution Experiments Powered by _breseq_ %BR%
*Adam Feist* %BR%
_University of California, San Diego_

<img src="%ATTACHURL%/aledb.png" width="120px">

%ICON{external}% [[https://aledb.org/][Visit the Adaptive Laboratory Evolution Database (ALEdb)]]

---+++ Zoom Workshop: Advanced Topics (July 22, 2021)

%ICON{mpeg}% [[https://utexas.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=e9ebfc4c-2682-4394-bf69-ad6f00df9c9b][Watch Recording]]

%ICON{pdf}% [[%ATTACHURL%/2021_Advanced_Workshop.pdf][Download Slides]]

%ICON{zip}% [[%ATTACHURL%/Advanced_Workshop_Files.zip][Download Examples]]

---+++ Zoom Workshop: Introductory Topics (July 20, 2021)

%ICON{mpeg}% [[https://utexas.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4c774614-17d4-4b81-b89c-ad6c00fbd4eb][Watch Recording]]

%ICON{pdf}% [[%ATTACHURL%/2021_Introductory_Workshop.pdf][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)
%BR%<code>breseq -l 80 -r REL606.gbk SRR2584524.fastq.gz</code>
%BR%[[https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/IntroWorkshop/REL11392_Ara+1_50K_clone_A/][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)
%BR%<code>breseq -p -l 80 -r REL606.gbk SRR2584524.fastq.gz</code>
%BR%[[https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/IntroWorkshop/REL11392_Ara+1_50K_clone_A_polymorphism/][View Results]]

Example 2: Results for another evolved clone that was sequenced with longer reads (LTEE Ara+1 50,000 generations, Clone B)
%BR%<code>breseq -r REL606.gbk SRR2584534_1.fastq.gz SRR2584534_2.fastq.gz</code>
%BR%[[https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/IntroWorkshop/REL11393_Ara+1_50K_clone_B/][View Results]]

Example 3: Analyzing the mixed population that both of these clones were isolated from (LTEE Ara+1 50,000 generations, Population)
%BR%<code>breseq -j 8 -p -r REL606.gbk SRR6173952_1.fastq.gz SRR6173952_2.fastq.gz</code>
%BR%[[https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/IntroWorkshop/REL11383_Ara+1_50K_population/][View Results]]

Example 4: Results from mapping to reference genome of a closely related strain–many predictions (links removed to save disk space).
%BR%<code>breseq -r NC_000913.3.MG1655.gbk SRR2584534_1.fastq.gz SRR2584534_2.fastq.gz</code>
%BR%[[https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/IntroWorkshop/REL11393_Ara+1_50K_clone_B_K12/][View Results]]

Example 5: Analyzing an _E. coli_ cell that contains a plasmid
%BR%<code>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</code>
%BR%[[https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/IntroWorkshop/Ecoli_with_plasmid/][View Results]]

Example 6a: Locating the insertion site of an integration cassette in the _A. baylyi_ genome using a junction reference (best option)
%BR%<code>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</code>
%BR%[[https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/IntroWorkshop/Abaylyi_with_cassette/][View Results]]

Example 6b: Same sample not using junction reference
%BR%<code>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</code>
%BR%[[https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/IntroWorkshop/Abaylyi_with_cassette_normal/][View Results]]

Example 6c: Same sample using targeted mode
%BR%<code>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</code>
%BR%[[https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/IntroWorkshop/Abaylyi_with_cassette_targeted/][View Results]]

Example 7a: Mapping to a de novo assembled reference
%BR%<code>breseq -r assembly.fasta SRR2584534_1.fastq.gz SRR2584534_2.fastq.gz</code>
%BR%[[https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/IntroWorkshop/REL11393_Ara+1_50K_clone_B_assembly/][View Results]]

Example 7b: Mapping to a de novo assembled reference using contig mode (best option)
%BR%<code>breseq -c assembly.fasta SRR2584534_1.fastq.gz SRR2584534_2.fastq.gz</code>
%BR%[[https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/IntroWorkshop/REL11393_Ara+1_50K_clone_B_assembly_contig/][View Results]]

---++ Feedback and Bug Reporting

Please report bugs on [[https://github.com/barricklab/breseq/issues][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. [[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=24838886][&laquo;PubMed&raquo;]]

| *Download Link* | *Size* | *Description* |
| [[%ATTACHURL%/Clonal_Sample.tgz][%ICON{download}% <literal>Clonal_Sample.tgz</literal>]] | 267M | Input files for clonal sample |
| [[%ATTACHURL%/Clonal_Output.tgz][%ICON{download}% <literal>Clonal_Output.tgz</literal>]] | 1.2M | Output files for clonal sample |
| [[%ATTACHURL%/Population_Sample.tgz][%ICON{download}% <literal>Population_Sample.tgz</literal>]] | 1.4G | Input files for time-course of population samples |
| [[%ATTACHURL%/Population_Output.tgz][%ICON{download}% <literal>Population_Output.tgz</literal>]] | 11M | Output files for time-course of population samples, including comparison |
| [[%ATTACHURL%/Mutation_Examples.tgz][%ICON{download}% <literal>Mutation_Examples.tgz</literal>]] | 199K | Examples of using unassigned evidence to predict complex mutations |
| [[%ATTACHURL%/Poor_Evidence_Examples.tgz][%ICON{download}% <literal>Poor_Evidence_Examples.tgz</literal>]] | 139K | Example output showing characteristics of poor evidence | 

---++ Other Resources

*Previous Versions:*
| %ICON{download}% [[http://barricklab.org/release/breseq][Previous versions from 0.24rc6 to 0.25d (barricklab.org)]] |
| %ICON{download}% [[http://code.google.com/p/breseq/downloads/list][Previous versions up to 0.24rc6 (Google Code)]] |

*Additional test data and an example of __breseq__ output:*
| [[%ATTACHURL%/REL8593A.fastq.gz][%ICON{download}% FASTQ reads for _E. coli_ strain REL8593A (200M)]] | 
| [[%ATTACHURL%/REL606.gbk.gz][%ICON{download}% Reference genome (REL606)]] |
| [[%ATTACHURL%/REL8593A_output][%ICON{external}% Example of __breseq__ output]] |
Barrick Lab > ToolList > ToolsBacterialGenomeResequencing
Topic revision: r59 - 2021-10-11 - 18:36:29 - Main.JeffreyBarrick