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runMapping (version 1.0.1)

Unpaired Reads Sff Files

Unpaired Reads Sff Files 0

Unpaired Reads Fasta/Fastq Files

Unpaired Reads Fasta/Fastq Files 0

Paired Reads Sff Files

Paired Reads Sff Files 0

Paired Reads Fasta/Fastq Files

Paired Reads Fasta/Fastq Files 0

[-paired_reads] If supplying paired reads (above), do you want paired-read info?:

[-pair] Output pairwise overlaps:

[-l] This option sets the minimum length for a contig to appear in the 454LargeContigs.fna file:

Reference Sequences

Reference Sequence 0

Reference type:

[-rst] Repeat score threshold parameter. Allowed values: 0 or greater:

[-hsl] Hit-per-seed limit parameter:

[-srv] Single read variant output:

[-mcf] Specify non-default MID config file:

[-fi] Include filter file to be specified:

[-fe] Exclude filter file to be specified:

[-vt] This option specifies a vector trimming database, or FASTA file of sequences to be used to trim the ends of input reads (for cloning vectors, primers, adapters or other end sequences):

[-vs] This option specifies a vector screening database, or FASTA file of sequences to be used to screen the input reads for contaminants. Reads that completely align against the screening database are trimmed completely (so that it is not used in the computation), but otherwise the read trimpoints are not changed:

[-minlen] Minimum length of reads to use (15-45 allowed):

[-notrim] Do not perform default quality and primer trimming of input reads:

[-tr] Output trimmed reads:

[-nor] Turn off the automatic rescore function for read quality scores:

[-ud] Treat each read separately, with no grouping of duplicates:

[-ss] Seed step parameter - The number of bases between seed generation locations used in the exact k-mer matching part of the overlap detection. Allow values: 1 or greater:

[-sl] Seed length parameter - The number of bases used for each seed in the exact k-mer matching part of the overlap detection (i.e. the 'k' value of the k-mer matching). Allowed values: 6-16:

[-sc] Seed count parameter - The number of seeds required in a window before an extension is made. Allowed values: 1 or greater:

[-ml] Minimum overlap length - The minimum length of overlaps used for the pairwise alignment step. The value can either be a minimum length in bases or a percentage of read length. In the case of a percentage, simply include '%' immediately following the numeric value. Allowed values: 1 or greater:

[-mi] Minimum overlap identity - The percent identity of overlaps used for the pairwise alignment step. Allowed values: 0 or greater:

[-ais] Alignment identity score - When multiple overlaps are found, the per-overlap column identity score used to sort the overlaps for use in the progressive alignment. Allowed values: 0 or greater:

[-e] This option tells the assembler that the expected depth of the data is at a certain level. The assembler has been optimized for datasets in the 10-50x oversampling size, and this option helps the assembler with datasets that have a higher oversampling level. A value of 0 resets the assembler computation to use its default algorithms:

[-no] Do complete assembly:

[-qo] Generate quick output for mapping and assembly. Disables signal distribution computation for calling consensus sequences and can decrease accuracy:

[-a] This option sets the minimum length for a contig to appear in the 454AllContigs.fna file.:

Output Alignment Info:

Produce Ace assembly file:

[-bam] Produce Bam alignments file: