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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’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.

Additionally, NextGENe’s whole genome alignment tool features complete annotation of the reference.
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 the Ion Torrent Proton™, Illumina GA, HiSeq and MiSeq; Roche FLX and Junior, and Applied BioSystems SOLiD System 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. In May 2009 researchers from The Wellcome Trust Sanger Institute published a paper detailing their novel BWT alignment method, BWA, which improved upon previous methods by allowing for the alignment of 51bp Illumina reads as well as SOLiD color-space reads.

For More Information Review or Download Application notes:
Whole Genome Alignment with NextGENe software
Paired end read merging with NextGENe software
Processing Paired End Sequencing Data from the Ion PGM™ Sequencer with NextGENe® Software
Reducing error of NGS Sequencing data with NextGENe Condensation™ Tool
NextGENe Illumina SNP_Indel_Detection
NextGENe SNP_ Indel_Discovery_SOLID
SNP_INDEL_detection_Roche454
Demultiplexing Illumina® MiSeq™ Data
Structural Variant Analysis
NextGENe software Variant Comparison Tool
Mutation Confidence Scoring with NextGENe software
NextGENe SNP & Indel Viewer
Deep Sequence Analysis with NextGENe software
Whole Genome Alignment with NextGENe software
Sequence Capture Analysis with NextGENe software
Paired end read merging with NextGENe software
Sequence Analysis Using Barcode/Index Tags of Pooled Samples with NextGENe Software
Using NextGENe software's Pipeline Automation Tool
Plugin for Torrent Browser automation

Review additional NextGENe software applications:

Pricing & Trial Version:
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Reference Material:
Download/View NextGENe® Brochure
NextGENe User Manual
Annotated Reference Genomes

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