Index

Symbols | B | G | R

Symbols

--format <PNG/PDF>
breseq_bam2cov command line option
--html
gdtools-ANNOTATE-(or-COMPARE) 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 <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
--html
-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