Index

Symbols

--bam breseq_bam2aln command line option breseq_bam2cov command line option --fasta breseq_bam2aln command line option breseq_bam2cov command line option --format breseq_bam2cov command line option gdtools-APPLY command line option --help breseq command line option --max-reads breseq_bam2aln command line option --name breseq command line option --nanopore breseq command line option --no-junction-prediction breseq command line option --num-processors breseq command line option --output breseq_bam2aln command line option breseq_bam2cov command line option gdtools-ANNOTATE-(or-COMPARE) command line option gdtools-APPLY command line option --predict-polymorphisms breseq command line option --reference breseq command line option gdtools-ANNOTATE-(or-COMPARE) command line option gdtools-APPLY command line option --region breseq_bam2aln command line option breseq_bam2cov command line option --resolution breseq_bam2cov command line option

--table breseq_bam2cov command line option --total-only breseq_bam2cov command line option -1 breseq_bam2cov command line option -b breseq_bam2aln command line option breseq_bam2cov command line option -f breseq_bam2aln command line option breseq_bam2cov command line option gdtools-ANNOTATE-(or-COMPARE) command line option gdtools-APPLY command line option -h breseq command line option -j breseq command line option -n breseq command line option breseq_bam2aln command line option -o breseq_bam2aln command line option breseq_bam2cov command line option gdtools-ANNOTATE-(or-COMPARE) command line option gdtools-APPLY command line option -p breseq command line option -r breseq command line option breseq_bam2aln command line option breseq_bam2cov command line option gdtools-ANNOTATE-(or-COMPARE) command line option gdtools-APPLY command line option -t breseq_bam2cov command line option -x breseq command line option

B

breseq command line option --help --name --nanopore --no-junction-prediction --num-processors --predict-polymorphisms --reference -h -j -n -p -r -x reads1.fastq reads3.fastq...] breseq_bam2aln command line option --bam --fasta --max-reads --output --region -b -f -n -o -r

breseq_bam2cov command line option --bam --fasta --format --output --region --resolution --table --total-only -1 -b -f -o -r -t

G

gdtools-ANNOTATE-(or-COMPARE) command line option --output --reference -f -o -r

gdtools-APPLY command line option --format --output --reference -f -o -r

R

reads1.fastq breseq command line option

reads3.fastq...] breseq command line option