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Index

A B C D E F G H I J K L M N O P Q R S T U V

a

  • aligned readings: sorted on alignment score
  • allcontigs list
  • allreadings list
  • Annotations: contig editor
  • Assembly
  • assembly problems: breaking contigs
  • assembly problems: disassembling readings
  • assembly problems: removing readings
  • Assembly: bwa aln
  • Assembly: bwa dbwtsw
  • Assembly: fasta/fastq
  • Assembly: tg_index
  • b

  • BASE_BRIEF_FORMAT1
  • BASE_BRIEF_FORMAT2
  • Break contig
  • bwa
  • c

  • Calculate consensus
  • Calculate consensus: algorithm
  • Calculate consensus: confidence
  • Calculate consensus: normal consensus
  • Calculate consensus: reliability
  • Change directory
  • Check assembly
  • Check database
  • Colour: contig editor highlight disagreements
  • Comparator window
  • Confidence of base calls
  • Confidence of consensus
  • configure: contig editor
  • Configure: restriction enzymes
  • Consensus calculation confidence
  • Consensus calculation method
  • consensus IUB codes
  • Consensus: contig editor
  • Consensus: outputting
  • Contig Comparator
  • Contig comparator: auto navigation
  • Contig Comparator: manipulating results
  • Contig comparator: next button
  • Contig Editor: alignment coordinates
  • Contig Editor: annotations
  • Contig Editor: cursor
  • Contig Editor: cutoff data
  • Contig Editor: cutoff values
  • Contig Editor: editing features
  • Contig Editor: editing keys
  • Contig Editor: Group Readings
  • Contig Editor: Highlight Disagreements
  • Contig Editor: highlighting readings
  • Contig Editor: information line
  • Contig Editor: joining
  • Contig Editor: multiple editors
  • Contig Editor: names display
  • Contig Editor: Primer selection
  • Contig Editor: quality values
  • Contig Editor: quitting
  • Contig Editor: saving configuration
  • Contig Editor: saving settings
  • Contig Editor: scrolling
  • Contig Editor: searching
  • Contig Editor: selecting sequences
  • Contig Editor: selections
  • Contig Editor: settings menu
  • Contig Editor: summary
  • Contig Editor: tags
  • Contig Editor: trace display
  • contig joining
  • contig naming
  • Contig order: Contig Selector
  • Contig Selector: changing the contig order
  • Contig Selector: Contig order
  • Contig Selector: menus
  • Contig Selector: saving the contig order
  • Contig Selector: selecting contigs
  • CONTIG_BRIEF_FORMAT
  • contigs - identifying
  • contigs list
  • Contigs to Readings: lists
  • Copy list
  • Create list
  • Cursor: contig editor
  • Cutoff data: contig editor
  • Cutoff values: contig editor
  • d

  • database creation
  • Delete Contigs
  • Delete list
  • Disassemble readings
  • Dots: contig editor highlight disagreements
  • e

  • Edit list
  • Editing: contig editor
  • Entering readings
  • error messages: find internal joins
  • error messages: maxseq
  • Export GFF
  • Export Sequences
  • Export Tags
  • f

  • Fasta output from Gap
  • File menu: Contig Selector
  • File of filenames generation
  • Find internal joins
  • Find internal joins: dialogue
  • Find oligos
  • Find read pairs
  • Find read pairs: display
  • Find repeats
  • Find sequences
  • finding joins
  • finding overlaps
  • g

  • GFF: exporting
  • GFF: importing from
  • Group Readings: contig editor
  • h

  • hidden data
  • Hidden data: contig editor
  • Hide, in Contig Comparator
  • Highlight Disagreements: contig editor
  • Highlighting readings in the editor
  • i

  • identifying contigs
  • Import GFF Annotations
  • Information line: contig editor
  • Information line: contig in contig editor
  • Information line: readings in contig editor
  • Information line: tags in contig editor
  • Information, in Contig Comparator
  • Insert Sizes
  • Invoke contig editors, in Contig Comparator
  • Invoke contig join editors, in Contig Comparator
  • IUB codes: consensus
  • j

  • Join Editor
  • joining contigs
  • k

  • Keyboard summary (contig editor)
  • l

  • List base confidence
  • List confidence
  • List Libraries
  • Lists
  • Lists: commands
  • Lists: Contigs to Readings
  • Lists: copy
  • Lists: create
  • Lists: delete
  • Lists: edit
  • Lists: load
  • Lists: print
  • Lists: save
  • Lists: search sequence names
  • Lists: special names
  • Load list
  • m

  • marking
  • masking
  • maxseq: find internal joins
  • n

  • names in the editor
  • naming contigs
  • Next button, in Contig comparator
  • Normal consensus
  • o

  • Oligo search
  • Oligo selection: contig editor
  • Open database
  • Output enzyme by enzyme: restriction enzymes plot
  • Output ordered on position: restriction enzymes plot
  • overlap finding
  • p

  • Primer Selection: contig editor
  • Print list
  • q

  • Quality calculation algorithm
  • Quality values: contig editor, use within
  • Quitting: contig editor
  • r

  • Read groups: SAM RG tags
  • Read pairs
  • READ_BRIEF_FORMAT
  • reading names in the editor
  • Reading names, searching for
  • reading percent mismatch
  • readings list
  • readings: sorted on alignment score
  • Remove Contig Holes
  • Remove Pad Columns
  • Remove, in Contig Comparator
  • Removing contigs
  • Removing readings
  • Removing results
  • Repeat search
  • Restriction enzymes
  • Restriction enzymes: configuring
  • Restriction enzymes: examining the plot
  • Restriction enzymes: selecting enzymes
  • Restriction enzymes: textual output
  • Results manager
  • Results manager: introduction
  • Results menu: Contig Selector
  • Results: removing
  • s

  • Save list
  • Search sequence names: lists
  • Searching: contig editor
  • selecting contigs: Contig Selector
  • Selecting sequences: contig editor
  • Selections: contig editor
  • Sequence names, searching for
  • Sequence Search
  • Settings menu: contig editor
  • Settings: saving in contig editor
  • Shuffle Pads
  • Sort Matches
  • Status line: contig editor
  • string search
  • Summary of editing commands: contig editor
  • Summary: contig editor
  • t

  • TAG_BRIEF_FORMAT
  • Tags: contig editor
  • Template Display
  • tg_index
  • Trace displays: contig editor
  • u

  • Unpadded base positions
  • v

  • View menu: Contig Selector

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    Last generated on 25 November 2011.