Alignment settings – .fasta or GenBank reference file

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The following alignment settings are available for .fasta sample files and BAM files with the Realignment option selected. If you load aligned BAM sample files without the Realignment option selected, then see BAM Sample Files settings.

Setting	Description
Matching Requirement: Base Number >= [x] and Base percentage >= [y]%	“x” indicates the minimum number of bases in each read that must match the reference sequence for the read to align with a specific position in the reference sequence. “y” indicates the minimum percentage of each sequence read that must match the reference sequence for the read to align with a specific position in the reference sequence. Note: Both conditions must be met for the read to be aligned to the position.
Allow Ambiguous Mapping	Aligns the read to each exact match position if a read matches exactly at more than one position in the reference. If this option is not selected, the read is aligned to the first exact match position from the start of the reference.
Remove Ambiguously Mapped Reads	Removes reads that match exactly to more than one position in the reference from the analysis.
Detect Large Indels	After an initial alignment is carried out, a consensus sequence is created and if an indel is found that occurs in at least 5% of the reads, this indel in reflected in the consensus sequence. The reads are then aligned again to this consensus sequence. Note: This option helps to align reads that include indels towards the end of the read, which in turn, allows allow for correctly calling the variant in the Mutation report. Processing time increases if this option is selected.
Rigorous Alignment	When this option is selected, after the matching region is determined for a read based on the matched bases and the uniqueness score, the alignment of individual bases is then checked to determine the alignment with the least mismatches. Consider the following simple example: AAAAAAAAAAGCTCGT AAAAAAAAAACGT - without rigorous alignment AAAAAAAAAA - - -CGT - with rigorous alignment Note: This option also helps to align reads that include indels.
Read length over reference length > [80%]	Displayed only for STR analysis and selected by default for STR analysis. The read must cover at least the indicate percentage of the segment to which it is aligned, or it is not assigned to an allele. See STR Analysis Project in the NextGENe Sequence Alignment Tool. Note: This setting ensures that the read covers an entire repeat region.