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emira

MIRA fragment assembly program (read the manual)

Unshaded fields are optional and can safely be ignored. (hide optional fields)

Input section
MIRA program parameters file (optional):
Parameter type

inappropriate datatype directory

inappropriate datatype directory

EXP assembly project file of filenames file:
PHD assembly project file of filenames file:
PHD assembly project sequences file:
Nucleotide sequences in FASTA format file:
Sequence read quality scores file:
CAF assembly project file:
MIRA program strain data file:
Sequence trace information file:
Required section
Basename for index files
Advanced section
Quality
Mapping quality
Grade
Highly repetitive DNA?
High quality data?
Preset EST assembly mode?
Preset horrid data set mode?
Preset EST assembly mode?
Job type
Filecheck only?
Merge XML trace info?
Scheme
Quality
External quality override?
Discard read on eq error?
Use template information?
Integer start step
Print date?
Load straindata?
Load backbone?
Start backbone usage in pass
Backbone strain name
File type
Backbone rail length
Backbone base quality
Also build new contigs?
Minimum read length
Number of passes
Skim each pass?
RMB break loops
Spoiler detection?
Spoiler detection last pass only?
Base default quality
Use genomic pathfinder?
Use emergency search stop?
Emergency search stop partner depth
Use max contig build time?
Build time in seconds
Use read extension?
Read extension window length
Read extension with max errors
First extension in pass
Last extension in pass
Tag poly-AT at ends?
Polybase window length
Polybase window max errors
Polybase window grace distance
Possible vector clip?
Possible vector clip max length allowed
Quality clip?
Quality clip minimum quality
Quality clip window length
Masked bases clip?
Masked bases clip gap size
Masked bases clip max front gap
Masked bases clip max end gap
Ensure minimum left clip?
Minimum left clip required
Set minimum left clip
Bases per hash
Hash saving step
Percent required
Max hits per read
Bandwidth in percent
Bandwidth minimum
Bandwidth maximum
Minimum overlap
Minimum score
Minimum relative score
Extra gap penalty?
Level
Maximum extra gap penalty percent
Name prefix
Level
Reject on drop in relscore
Danger max error rate
Mark repeats?
Assume SNP instead of repeat?
Minimum reads per group
Minimum group quality for RMB tagging
Endread mark exclusion area
Also mark gap bases?
Also mark gap bases, even multi-column?
Also mark gap bases, need both strands?
Default insert size minimum
Default insert size maximum
Automatic contig editing?
Strict editing mode?
Confirmation threshold
Output CAF results?
Output GAP4 results?
Output FASTA results?
Output ACE results?
Output TXT results?
Output TCS results?
Output HTML results?
Output temporary CAF results?
Output temporary GAP4 results?
Output temporary FASTA results?
Output temporary ACE results?
Output temporary TXT results?
Output temporary TCS results?
Output temporary HTML results?
Output extra temporary CAF results?
Output extra temporary GAP4 results?
Output extra temporary FASTA results?
Output extra temporary ACE results?
Output extra temporary TXT results?
Output extra temporary HTML results?
Text characters per line
HTML characters per line
Output section
GAP4 direct assembly directory name
Log files directory
Output file for a CAF project
Run section
Email address: If you are submitting a long job and would like to be informed by email when it finishes, enter your email address here.