Index

Symbols

--format <PNG/PDF> breseq_bam2cov command line option --no-junction-prediction breseq command line option --resolution <int> breseq_bam2cov command line option -1, --total-only breseq_bam2cov command line option -b <file_path>, --bam <file_path> breseq_bam2aln command line option breseq_bam2cov command line option -f <file_path>, --fasta <file_path> breseq_bam2aln command line option breseq_bam2cov command line option -f <format>,--format <format> gdtools-ANNOTATE-(or-COMPARE) command line option -f <output_format>, --format=<output_format> gdtools-APPLY command line option -h, --help breseq command line option -j <int>, --num-processors <int> breseq command line option

-n <int>, --max-reads <int> breseq_bam2aln command line option -n <string>, --name <string> breseq command line option -o <file_path>, --output=<file_path> gdtools-ANNOTATE-(or-COMPARE) command line option gdtools-APPLY command line option -o <path>, --output <path> breseq_bam2aln command line option breseq_bam2cov command line option -p, --predict-polymorphisms breseq command line option -r <file_path>, --reference <file_path> breseq command line option -r <file_path>, --reference=<file_path> gdtools-ANNOTATE-(or-COMPARE) command line option gdtools-APPLY command line option -r <region> , --region <region> breseq_bam2aln command line option -r <region>, --region <region> breseq_bam2cov command line option -t, --table breseq_bam2cov command line option

B

breseq command line option --no-junction-prediction -h, --help -j <int>, --num-processors <int> -n <string>, --name <string> -p, --predict-polymorphisms -r <file_path>, --reference <file_path> reads1.fastq [reads2.fastq, reads3.fastq...] breseq_bam2aln command line option -b <file_path>, --bam <file_path> -f <file_path>, --fasta <file_path> -n <int>, --max-reads <int> -o <path>, --output <path> -r <region> , --region <region>

breseq_bam2cov command line option --format <PNG/PDF> --resolution <int> -1, --total-only -b <file_path>, --bam <file_path> -f <file_path>, --fasta <file_path> -o <path>, --output <path> -r <region>, --region <region> -t, --table

G

gdtools-ANNOTATE-(or-COMPARE) command line option -f <format>,--format <format> -o <file_path>, --output=<file_path> -r <file_path>, --reference=<file_path>

gdtools-APPLY command line option -f <output_format>, --format=<output_format> -o <file_path>, --output=<file_path> -r <file_path>, --reference=<file_path>

R

reads1.fastq [reads2.fastq, reads3.fastq...] breseq command line option