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
Last generated on 25 November 2011.