Usage Summary ============== :program:`breseq` ------------------ Usage:: breseq -r reference1.gbk [-r reference2.gbk ...] reads1.fastq [reads2.fastq, reads3.fastq...] .. program:: breseq Run the :program:`breseq` mutation prediction pipeline. Required options: .. option:: -r , --reference 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. .. option:: 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: .. option:: -h, --help Produce help message showing advanced options. .. option:: -n , --name Human-readable name of the analysis run for output (DEFAULT=). .. option:: -j , --num-processors Number of processors to use in multithreaded steps (DEFAULT=1). .. option:: --no-junction-prediction Do not predict new sequence junctions. .. option:: -p, --predict-polymorphisms Predict polymorphic (mixed) mutations. .. option:: -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. 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 ...] .. program:: breseq_bam2aln Display reads aligned to the specified region or regions. Commonly used options: .. option:: -b , --bam BAM database file of read alignments (DEFAULT=data/reference.bam). .. option:: -f , --fasta FASTA file of reference sequences (DEFAULT=data/reference.fasta). .. option:: -o , --output 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=.). .. option:: -r , --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. .. option:: -n , --max-reads 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 ...] .. program:: breseq_bam2cov Create a coverage plot or table for the specified region or regions. Commonly used options: .. option:: -b , --bam BAM database file of read alignments (DEFAULT=data/reference.bam). .. option:: -f , --fasta FASTA file of reference sequences (DEFAULT=data/reference.fasta). .. option:: -o , --output 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=.). .. option:: -r , --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. .. option:: --format Format of output plot: PNG or PDF. (DEFAULT=PNG). .. option:: -t, --table Create tab-delimited file of coverage instead of a plot. .. option:: -1, --total-only Only plot/tabulate the total coverage at a position. That is, do not not output the coverage on each genomic strand. .. option:: --resolution Number of positions to output coverage information for in interval (0=ALL) (DEFAULT=600).