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Include Consensus – If this check box is selected, the application will generate all the output files, including the output files related to the generation of contigs and consensus sequence information. If it is not selected, the application will perform the mapping and will output files (454PairAlign.txt, 454ReadStatus (without locations in reference to what reads map) and 454TrimStatus) associated with the creation of the multiple-alignments, but will not output files (454AllContigs.fna and .qual, 454LargeContigs.fna and .qual, diff, rearrangement and variation files, etc.) or metrics (latter parts of 454NewblerMetrics.txt) involved with contig,consensus or variation information. If this option is unchecked, the mapping will run faster, providing an approximate idea of the quality of the data, based on the percentage of reads mapped.

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Quick output option generates output faster than using the default setting by disabling the “Computing signals…” computation. The default behavior of the mapper requires that all reads be re-read so that signal and quality information can be used to compute consensi (see Section 1.1). If this option is selected, the accuracy of the consensus may be degraded (i.e., more consensus errors may be generated) as the distribution statistics are not generated to assist in the basecalling step.

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Full variant file details – If this check box is selected, the application will output additional columns to the 454HCDiffs. txt and 454AllDiffs.txt files. See section 454AllDiffs.txt for details.

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Output trimmed reads – select this option to output the read sequences to a .fna file after trimming has been performed (includes vector / primer / Paired End linker / MIDs / low quality trimming). If available, the quality value for the output reads will be placed in a .qual file.

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The ACE Format option determines whether or what form of ACE file(s) are output by the application. The default is “Single ACE file for small genomes”. See section 2.17.1.5 for a description of the 454Contigs.ace file and of the ace and consed directories. By default, files consistent with version 17.0 or higher of consed are generated.

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The BAM option

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The Alignment Info option has 3 possible settings.

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Output – turns on generation of the 454AlignmentInfo.tsv file

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Output small – the file will be generated unless there are more than 4 M reads or the mapping generates contigs with a total length in excess of 40 Mbp.

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Pairwise Alignment – Determines whether the 454PairAlign.txt file is output; this file contains the overlaps used by the mapper.

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Default is “None”. See section 2.17.1.8 for a description of the 454PairAlign.txt file.

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Ace read mode – When the ACE file is generated, output reads using either the raw, complete basecalled read or using just the trimmed portion of the reads (after low quality, vector and key trimming)

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Single Read Variant – By default, variations of at least 2 reads relative to the reference are output. If this option is selected, variations supported by only a single read are also included.

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All contig threshold – The minimum number of bases for a contig to be output in the 454AllContigs.fna file

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Minimum contig depth – regions of references covered by at least this many reads are considered contigs for output purposes