BreSeq

BreSeq (SV caller)

• Author: Dreycey Albin
• Date: 05/10/2019
• Updated: 05/12/2019 -- finished
• BreSeq is used for finding structural variants
• documentation (website): breseq Github
• documentation (manual): BreSeq Manual
• documentation (publication): BRESEQ PUBLICATION

Installation

INSTRUCTIONS ON HOW TO INSTALL USING TERMINAL http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/installation.html

• installation for MacOS N/A
• installation for Linux

wget https://github.com/barricklab/breseq/releases/download/v0.33.2/breseq-0.33.2-Linux-x86_64.tar.gz
tar -zxvf breseq-0.33.2-Linux-x86_64.tar.g
cd breseq-0.33.2-Linux-x86_64

*set up env variables

echo "export PATH=\$PATH:${PWD}/bin" >> ~/.bashrc
echo "export PATH=\$PATH:${PWD}/bin/breseq" >> ~/.bashrc
source ~/.bashrc

Basic commands

INPUT

Using Breseq

breseq -r reference1.gbk [-r reference2.gbk ...] reads1.fastq [reads2.fastq, reads3.fastq...]

OUTPUT

• several directories and files
• Of particular note: there is a resulting .vcf

Example_1

Input files

• The input is read fastq files, and a reference genome -->
• obtain reference genome

wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/765/GCF_000006765.1_ASM676v1/GCF_000006765.1_ASM676v1_genomic.fna.gz;
gzip -d GCF_000006765.1_ASM676v1_genomic.fna.gz

• get illumina reads

wget http://resources.qiagenbioinformatics.com/testdata/paeruginosa-reads.zip;

commands

• Here is the command using the files used as input for Bowtie

breseq -p -j 4 -o dreyout -r ../Bowtie2/GCF_000006765.1_ASM676v1_genomic.fna ../Bowtie2/paeruginosa-reads/SRR396636.sra_1.fastq ../Bowtie2/paeruginosa-reads/SRR396636.sra_2.fastq

Output files

• Below are all of the directories and output files created by breseq

01_sequence_conversion:
sequence_conversion.done  summary.json

02_reference_alignment:
alignment.done

03_candidate_junctions:
candidate_junction.done coverage.summary.json
candidate_junction_summary.json error_count.summary.json
coverage_junction_alignment.done  preprocess_junction_alignment.done

04_candidate_junction_alignment:
candidate_junction_alignment.done

05_alignment_correction:
alignment_resolution.done  summary.json

06_bam:
bam.done

07_error_calibration:
0.unique_only_coverage_distribution.tab  error_rates.done
0.unique_only_coverage_distribution.tab.r.log  error_rates.tab
base_qual_error_prob.SRR396636.sra_1.tab SRR396636.sra_1.plot_error_rate.log
base_qual_error_prob.SRR396636.sra_2.tab SRR396636.sra_2.plot_error_rate.log
error_counts.done  summary.json
error_counts.tab

08_mutation_identification:
error_counts.tab polymorphism_statistics_output.log
mutation_identification.done polymorphism_statistics_output.tab
NC_002516.2.coverage.tab ra_mc_evidence.gd
polymorphism_statistics.done ra_mc_evidence_polymorphism_statistics.gd
polymorphism_statistics_input.tab

data:
output.gd  reference.bam.bai  reference.gff3 summary.json
output.vcf reference.fasta  SRR396636.sra_1.unmatched.fastq
reference.bam  reference.fasta.fai  SRR396636.sra_2.unmatched.fastq

output:
**calibration** index.html  marginal.html  output.gd
**evidence** log.txt output.done  summary.html

Example 2:

commands

• Use the provided .sh file/example

./run_tests.sh

Output files

breseq -p -j 4 -o dreyout -r ../Bowtie2/GCF_000006765.1_ASM676v1_genomic.fna ../Bowtie2/paeruginosa-reads/SRR396636.sra_1.fastq ../Bowtie2/paeruginosa-reads/SRR396636.sra_2.fastq