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Usage breseq
breseq -r reference1.gbk [-r reference2.gbk ...] reads1.fastq [reads2.fastq, reads3.fastq ...]
Run the breseq mutation prediction pipeline.
Required options:
-r <file_path>, --reference <file_path>
Input reference genome sequence files in GenBank, GFF3, or FASTA format. If there are multiple reference sequences stored in separate files (e.g., a bacterial genome and a plasmid), this option can be supplied multiple times.
reads1.fastq [reads2.fastq, reads3.fastq ...]
The remaining arguments at the command line are the FASTQ input files of reads. FASTQ files with base quality scores that are not in SANGER format will be converted. In addition, reads with >50% N bases will be removed from the converted FASTQ file by default. _breseq re-calibrates the error rates for each FASTQ file separately, so data sets that were generated independently should be stored in different input files.
Commonly used options:
-h, --help
Produce help message showing advanced options.
-n <string>, --name <string>
Human-readable name of the analysis run for output (DEFAULT=<none>).
-j <int>, --num-processors <int>
Number of processors to use in multithreaded steps (DEFAULT=1).
--no-junction-prediction
Do not predict new sequence junctions.
-p, --predict-polymorphisms
Predict polymorphic mutations. Add this option when you are analyzing mixed population (metagenomic) samples.
-x, --nanopore
Set read alignment and mutation calling options for Nanopore sequencing data. Important: no indel mutations will be called in homopolymer repeats of 4 or more bases with this option.
Tip
For a complete list of options (including many advanced options), please show the full command line help by running breseq -h or breseq --help.
breseq provides some additional subcommands for further analysis. The subcommands should be used after the main pipeline has been run. It is easiest to run them from within the main output directory of a breseq run, which will include the required data/reference.fasta and data/reference.bam files, so that you don't have to specify these options on the command line.
Usage:
breseq BAM2ALN [-b reference.bam -f reference.fasta -o alignment.html -n 200] region1 [region2 region3 ...]
Create an HTML file displaying reads aligned to the specified region or regions.
Commonly used options:
-h, --help
Produce help message showing advanced options.
-b <file_path>, --bam <file_path>
BAM database file of read alignments (DEFAULT=data/reference.bam).
-f <file_path>, --fasta <file_path>
FASTA file of reference sequences (DEFAULT=data/reference.fasta).
-o <path>, --output <path>
Output path. If there is just one region, the name of the output file
(DEFAULT=region1.). If there are multiple regions, this argument must
be a directory path, and all output files will be output here with names
region1., region2.*, ... (DEFAULT=.).
-r <region> , --region <region>
Regions to create alignments for. Must be provided as sequence regions in the format ACCESSION:START-END, where ACCESSION is a valid identifier for one of the sequences in the FASTA file, and START and END are 1-indexed coordinates of the beginning and end positions. Any read overlapping these positions will be shown. A separate output file is created for each region. Regions may be provided at the end of the command line as unnamed arguments.
-n <int>, --max-reads <int>
Maximum number of reads that will be aligned to a region. If there are more than this many reads, then the reads displayed are randomly chosen and a warning is added to the output. (DEFAULT=200).
Usage:
breseq BAM2COV [-b reference.bam -f reference.fasta --format PNG -o output.png] region1 [region2 region3 ...]
Create a coverage plot or table for the specified region or regions.
Commonly used options:
-h, --help
Produce help message showing advanced options.
-b <file_path>, --bam <file_path>
BAM database file of read alignments (DEFAULT=data/reference.bam).
-f <file_path>, --fasta <file_path>
FASTA file of reference sequences (DEFAULT=data/reference.fasta).
-o <path>, --output <path>
Output path. If there is just one region, the name of the output file
(DEFAULT=region1.*). If there are multiple regions, this argument must
be a directory path, and all output files will be output here with names
region1.*, region2.*, ... (DEFAULT=.).
-r <region>, --region <region>
Regions to create alignments for. Must be provided as sequence regions in the format ACCESSION:START-END, where ACCESSION is a valid identifier for one of the sequences in the FASTA file, and START and END are 1-indexed coordinates of the beginning and end positions. Any read overlapping these positions will be shown. A separate output file is created for each region. Regions may be provided at the end of the command line as unnamed arguments.
--format <PNG/PDF>
Format of output plot: PNG or PDF. (DEFAULT=PNG).
-t, --table
Create tab-delimited file of coverage instead of a plot.
-1, --total-only
Only plot/tabulate the total coverage at a position. That is, do not not output the coverage on each genomic strand.
--resolution <int>
Number of positions to output coverage information for in interval (0=ALL) (DEFAULT=600).
Quick Start
Installation
Test Drive
More Options
Usage: breseq
Usage: gdtools
More Information
GenomeDiff File Format
Reference Sequence File Formats
Output
Methods
Bibliography
FAQ
More Examples
Tutorial: Clones
Tutorial: Populations
Tutorial: Barcoded/Targeted
Tutorial: Curation
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