Usage Summary

breseq

Usage:

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 (mixed) mutations.

For a complete list of options, please see the command line help (by using the -h option).

Command: bam2aln

Usage:

breseq BAM2ALN [-b reference.bam -f reference.fasta -o alignment.html -n 200] region1 [region2 region3 ...]

Display reads aligned to the specified region or regions.

Commonly used 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).

Command: bam2cov

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:

-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).