Whole Genome Alignment

SoftGenetics has developed for NextGENe software a modified Burrows-Wheeler transform (BWT) alignment method that includes several improvements over other methods to generate fast accurate alignment of sequence reads to a whole large genome reference such as the human genome with high accuracy and speed.

NextGENe software's whole genome alignment algorithm is a multi-step process that first aligns perfectly matching reads, then reads with a user set number of mis-matches and finally it breaks the remaining reads into seeds. The algorithm then aligns reads to a large genome by matching seeds smaller than the read length and then extending the alignment to find the best matching position for the whole read. This allows for the alignment of long reads and reads with indels.

The NextGENe whole genome alignment method uses an indexed reference sequence. Indexed references with full annotation are available for many genomes including the human genome, mouse genome, and many more. A tool for building custom indexed reference is also included. Alignment of high throughput short sequence reads to a large reference genome like the human genome is a difficult challenge.

The Burrows-Wheeler transform is a widely accepted data compression algorithm that has been in use since 1994. Massively parallel sequencers such as Illumina® iSeq, Miniseq, MiSeq, NextSeq, HiSeq, and NovaSeq systems, Ion Torrent Ion GeneStudio S5, PGM, and Proton systems as well as other platforms are capable of producing millions or billions of reads per run, which has led to an interest in the usage of BWT algorithm to align this large volume of sample reads to entire genomes. The algorithm has been successfully used for this purpose by alignment programs such as Bowtie and BWA.

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