Name

Description

Parameter Name

Parameter Description

Examples

assemblePairs

Takes any legal file spec, folder, file of files, or a single sequence and tries to assemble it with its pair if the pair is in the assembly.

file:"aFileSpec.fof"

blastContigs

To perform a BLAST search of the specified contigs.

Any valid contig specifier

See Specifying contigs.

blastContigs

          contigs: {1}

          file: "pathname\BLASTresultsfile"

file

The directory and filename for the BLAST results file. The pathname and filename you wish to save must be enclosed in quotes.

complementContigs

Same as the Contig > Complement Contig menu command.

Any valid contig specifier

See Specifying contigs.

complementScaffolds

To reverse complement all contigs within a specific scaffold. The order of the contigs in the scaffold is also reversed. Choose from one of the following parameters.

scaffolds:located

Complements scaffolds that have a specified location.

scaffolds:{10,20}

Complements one or more scaffolds specified by ID.

scaffolds:all

Complements all scaffolds.

scaffolds:none

Complements no scaffolds.

copyFeaturesToConsensus

To copy the features from a sequence in your project (such as the reference) to the consensus sequence.

Any valid contig specifier

See Specifying contigs.

To copy the features on your reference sequence to the consensus from all of the contigs in your project:

copyFeaturesToConsensus

          contigs:all

sequenceName:"RefSeqName.seq"

sequenceName:"sequence name"

Specifies the name of the sequence from which the features should be copied. The sequence name must be enclosed in quotes.

deleteContigs

Same as the Contig > Delete Contig menu command. Deletes contigs from the project.

Any valid contig specifier

See Specifying contigs.

To delete contigs having only one sequence:

deleteContigs

          contigs:where {number<=1})

deleteSequence

Same as the Sequence > Delete menu command. Removes one or more sequences from a project.

SeqMan accepts the addition of sequences with the same name to a project, including the addition of the same sequence multiple times. The deleteSequence command deletes only the first instance of the named sequence(s) from the project, if the named sequence is found. The deleteSequencesFrom command deletes the first instance of the named sequence if the named sequence is found in the specified contig(s).

sequences:{"filename1.ext" "filename2.ext"}

The name value for each sequence must be enclosed in quotes.

To delete the first instance of Sequence 1, wherever it may appear in the assembly:

deleteSequence

          sequences:{"sequence1.abi"}

deleteSequencesFrom

To delete the first instance of the named sequence if the named sequence is found in the specified contig(s).

contigs:{1 2 3}

Defines the contigs from which the specified sequence(s) will be deleted.

To delete the first instances of Sequence 3 (if found) from Contigs 2:

deleteSequenceFrom

          contigs:{2}

          sequences:{"sequence3.abi"}

sequences:{"filename1.ext" "filename2.ext"}

Defines the sequences you wish to delete if they are found in specific contigs. The name value for each sequence must be enclosed in quotes.

exportPrimerInfo

Same as the Contig>Primer Walk menu command. Exports the Primer Walking Report.

Any valid contig specifier

See Specifying contigs.

file:"pathname\filename"

Specifies the location and name for the output file. The pathname\filename must be enclosed in quotes.

Specify the format for the output file by choosing at least one of the following parameters:

format:text

Exports the data from the primer walking report as a tab-delimited text file (.txt).

format:fasta

Exports the primer sequences from the primer walking report as a FASTA file (.fas).

primerType:extension

Specifies that SeqMan will search for primers that walk into gaps, priming locations at the ends of contigs, polymerizing into gaps between them.

primerType:coverage

Specifies that SeqMan will search for primers that improve coverage, priming locations that surround areas of low coverage.

If no primerType parameter is specified, SeqMan will search for both types of primers (extension and coverage).

targetTm:60.0

Represents the value for melting temperature that will become the target for the entire set of results. Optimal primers will be chosen as close to this value as possible, provided they meet the other constraints. Default 60.

minCoverage: 4

This value determines the upper bound on locations that will be considered for coverage improvement. Areas that are deeper than this value will be excluded from the search. Default 4.

coverageStrand: both

Applies the minCoverage value to the minimum of the depth on one strand.

coverageStrand: either

Applies the minCoverage value to the overall depth of the contig.

alternatePrimers: 0

The number of alternative primers you wish to search for. Increasing this value causes the search algorithm to present additional primers whose role in extension or coverage overlaps the most optimal choice. The number of primers presented for a given purpose is equal to this value plus one. Default 0.

backAwayFromEnds: 50

This parameter weights the location of primers maximally at the distance specified from the contig ends, tapering linearly in either direction. The value overrides the confidence in the quality of sequence reads near their ends forcing greater overlaps when the value is increased. Default 50.

mustCoverClones: false

Value may be true or false. When true, SeqMan forces primers to be considered only when at least one sequence read overlaps the primer location on the strand being primed. Default False.

uniqueLen: 12

The value for this parameter represents the length that defines uniqueness for 3’ dimerization with the template. Default 12.

falsePrimers: disallow

Value may be allow or disallow. When disallow is used, SeqMan will not accept false priming, unless it occurs within the distance from sequence ends specified for the ignoreFalseDistance parameter. Default Disallow.

ignoreFalseDistance: 500

The distance from sequence ends where false priming sites may still occur if falsePrimers parameter is set to disallow. Default 500.

absentFromSeq: "pathname\filename.ext"

Specifies the file for a vector or contaminant sequence which must not prime a polymerization. The pathname\filename must exist, must have a valid sequence extension replacing the “.ext” extension, and must be enclosed in quotes.

minLength: 18

Specifies the shortest acceptable primer length in bases. Default 18.

maxLength: 24

Specifies the longest acceptable primer length in bases. Default 24.

salt: 50

Specifies the millimolar concentration of salt (Na) at the start of polymerization. Default 50.

formamide: 0

Specifies the concentration of formamide express as a percentage in solution. Default 0.

dGTemp: 25.0

Specifies the temperature for Delta G calculations for thermodynamic modeling. Default 25.

hairpins: disallow

Value may be allow or disallow. When disallow is specified, primers that fold and bond to themselves will be avoided. Default Disallow.

dimers: disallow

Value may be allow or disallow. When disallow is specified, primers that hybridize to themselves will be avoided. Default Disallow.

duplexLimit: 8

Specifies the distance in bases from the 3’ end of the primer where hairpin formation and self-hybridization may be ignored. Default 8.

extendEnds

To restore sequence ends at the beginning and end of a contig.

Any valid contig specifier

See Specifying contigs.

joinContigs

To force join two contigs.

Choose from one of the following two parameters:

This script will join contigs 1 and 2 at offset 67. As with the Contig > Force Join Contigs command, this will lead to a join whether or not sequence similarity would permit joining:

joinContigs

          contigs:{1 2}

          offset: 67

          method:force

contigs:{1 2}

This expression allows you to specify contigs by contig number.

sequencesInContigs:{filename1.ext filename2.ext}

This expression allows you to specify contigs by naming the sequences they contain.

Optional parameters:

offset:67

This parameter lets you enter the number of base pairs that you wish the contigs to overlap. To evaluate alignment possibilities using sequence similarity without forcing a join at a specific location, omit this parameter.

method:align

This parameter causes the contigs to be joined only if their alignment score is higher than the Minimum Match Percentage.

method:force

This parameter causes the contigs to be joined regardless of whether their alignment score is higher than the Minimum Match Percentage.

locateContigs

To manually create a scaffold of the specified contigs.

To place one or more contigs into a particular scaffold, include the group (i.e., scaffold) parameter. To order one or more contigs within a particular scaffold, include the position parameter. The group and position parameters must be specified on different lines.

Any valid contig specifier

See Specifying contigs.

Example 1: To assign positions to multiple contigs, use a separate locateContigs statement for each contig:

locateContigs

          contigs:{1} position:{10}

locateContigs

          contigs:{9} position:{20}

Example 2: To assign multiple contigs to a single scaffold and specify a position for one of the contigs:

locateContigs

          contigs:{1 3} group:{4}

          contigs:{1} position:{40}

group

The scaffold in which to place one or more contigs.

position

The order for the contig in the scaffold.

locateScaffolds

To manually join scaffolds together.

To assign positions to multiple contigs, use a separate locateContigs command for each contig.

Any valid contig specifier

See Specifying contigs.

locateScaffolds

          scaffolds:{1} position:{10}

lockContigs

To lock a contig.

Locked contigs may not be changed in any way. For example, new data may not be assembled into locked contigs and sequences may not be deleted from them.

Any valid contig specifier

See Specifying contigs.

mergeProject

To add contigs from a saved SeqMan project to the current project.

file:"pathname\filename.sqd"

The directory and filename of the project you wish to merge with the current project must be enclosed in quotes and terminate with the extension “.sqd”.

nameContig

To name a single contig.

contigs:{10}

The name of the specific contig that you want to rename.

nameContig

          contigs: {20}

          name: "25"

In the example above, Contig 20 will be renamed to Contig 25.

name: "new name for contig"

The new name for the specified contig.

reassemble

To reassemble contigs.

contigs:{10, 20}

The contigs you specify are reassembled. In this case, contigs 10 and 20 will be reassembled.

resetSetEnds

To restore the original endpoints for all unassembled sequences.

(None available)

splitContig

To split a contig either at a specific position or based on coverage.

Any valid contig specifier

See Specifying contigs.

Example 1: This example splits contig 1 at position 689:

splitContig

          contigs:{1} position:{689}

Example 2: This example splits contig 1 in areas where the coverage meets or exceeds the following coverage parameter values: Coverage Threshold = 4, Minimum Number on Each Strand = 2, and Maximum Expected Coverage = 100.

splitContig

          contigs:{1}

coverageThresh:{4 2 100}

coverageType:exceedCoverage

position

The coordinate of the contig where it should be split.

coverageThresh

This parameter allows you to specify values for the three Strategy Viewing & Coverage Parameters that SeqMan should use to split the contig based on coverage: Coverage Threshold, Minimum Number on Each Strand, and Maximum Expected Coverage. (Also see coverageType below.)

coverageType

The type of coverage SeqMan should use to split the contig. Acceptable values are:

•      single - Areas where coverage is by a single read only.

•      singleDir - Areas where coverage is on one strand only.

•      belowThresh - Areas that fall under the specified coverageThresh requirements. (See parameter above.)

•      noCoverage - Areas that have zero coverage.

•      exceedCoverage - Areas that meet or exceed the specified coverageThresh requirements.

unlockContigs

To unlock a contig.

Any valid contig specifier

See Specifying contigs.