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Novocraft Touts Sequence Alignment Software's Accuracy as Key Differentiator in NGS Marketplace


By Uduak Grace Thomas

Novocraft, a Malaysian-based bioinformatics software vendor, is hoping that the improved accuracy of its alignment software, Novoalign, will reel in new customers in the next-generation sequence data analysis space.

Novoalign is a short-read alignment software program that lets users align single-end and paired-end reads from Illumina and Roche 454 sequencers.

Features include an alignment mode for bisulfite sequencing data; base quality calibration during the alignment process to improve sensitivity and specificity; multithreading capabilities; and adapter trimming for paired-end and short RNA reads.

Zayed Albertyn, Novocraft's bioinformatics director, told BioInform this week that the software, which is based on the Needleman-Wunsch algorithm, is more sensitive when it comes to selecting correct alignments for reads and identifying false positives than some well-known open source tools like the Burrows-Wheeler Aligner and Bowtie, which he considers the biggest threat to his firm's business.

Some recent independent publications support Albertyn's claims. For example, researchers from India's Ganit Labs and Strand Life Sciences published a PLoS One paper in January that compared the abilities of several aligners including Novoalign, Bowtie, and Stampy.

According to the paper, Novoalign and Stampy were able to "maintain a consistently high-quality score across different variant callers" when the researchers looked at the average base quality score of variants.

Furthermore, they wrote, Novoalign produced "equally good variant quality no matter which downstream variant caller is used" a feat that they attributed to "a post-alignment base quality recalibration method" that Novoalign uses. This is compared to Stampy, which "yielded good quality scores for all variant callers, albeit with varying frequency," although it also uses a post alignment base-recalibration approach.

A separate study published in Bioinformatics last year by researchers affiliated with the Max Planck Institute for Molecular Genetics looked at how MAQ, RazerS, Bowtie, BWA, and Novoalign aligned simulated datasets containing insertions and deletions.

Among other results, the researchers found that BWA was only able to map about 80 percent of reads from regions without indels, compared to 98 percent for Novoalign and RazerS. Of the indel-free mapped reads, Novoalign and BWA were able to map about 99 percent of reads to their correct coordinates compared to about 95 percent by RazerS.

Furthermore, an indel detection algorithm was able to detect about 90 percent of indels in reads mapped by Novoalign compared to about 50 percent in reads mapped by BWA, the paper said.

In addition to Novoalign, Novocraft markets NovoalignCS, which is used to align color space reads generated by Life Technologies' SOLiD sequencers.

NovoalignCS features include support for single-end and mate-pair read libraries; color quality calibration; Phred style scoring and alignment qualities; and iterative read trimming until reads align.

Novocraft also offers message passing interface versions of both Novoalign and NovoalignCS, which lets researchers align reads using multiple servers in a compute cluster.

Also included in both tool suites are NovoMethyl, a methylation caller for bisulfite alignments; and Novobarcode, a program that de-multiplexes reads where several samples, each with a unique index tag, have been sequenced in a single lane.

Customers can use a free version of Novoalign that offers access to a limited number of features and runs on a single compute core; or they can purchase licenses to the commercial version, which runs on multiple cores and includes additional features, for $1,000 per lab. The company also offers premium pricing options to larger institutions and corporations, Albertyn said.

Currently, NovoalignCS is only available with a license.

Meanwhile, Novocraft hopes to grow its business this year through new partnerships and by establishing a US-based office to provide better support for its North American clients who currently make up the largest fraction of its customer base, Albertyn told BioInform.

Novocraft has sold more than 160 licenses for its software tools to pharmaceutical and biotechnology companies as well as academic institutes.

Current customers include Monsanto; Roche; GlaxoSmithKline; the National Cancer Institute; the National Institutes of Health; Cold Spring Harbor Laboratory; Stanford University; the University of California, San Francisco; and the Ontario Institute for Cancer Research.

Moving forward, the company plans to develop additional tools and to continue making improvements to its existing software, Albertyn said.

For example, the company has made changes to some of its alignment processing including a new multi-fitted BAM sorting program called NovoSort, which prevents memory crashes associated with large alignment files, he said.

The company has also added features to its software that allow it to support data from Ion Torrent, Pacific Biosciences, and Helicos sequencers, he said.

Novocraft is also pursuing investment opportunities that would enable it to add to its headcount, which currently stands at eight; set up its US-based office; as well as advertise its services business better.

Novocraft offers services for CHIP-seq, miRNA/small RNA, RNA-seq, DNA methylation, and whole-genome sequencing; automated genome annotation; and variation detection.

Have topics you'd like to see covered in BioInform? Contact the editor at uthomas [at] genomeweb [.] com.