Lasergene Genomics Suite seamlessly assembles and analyzes Ion Torrent sequencing data, making it the perfect complement for Ion Torrent users. Our software runs at unprecedented speed, even on low-cost desktop computers, enabling researchers to prepare a sample, generate sequence data, and assemble and analyze their data in a single day. DNASTAR Lasergene software supports the following Ion Torrent project types:
- De novo genome assemblies
- De novo transcriptome assemblies
- Reference-guided genome alignments
- Targeted amplicon re-sequencing, including support for the Ion AmpliSeq™ Cancer Panel
- Assembly and analysis of gene panel data
- Whole genome/whole exome validation
- ChIP-Seq, RNA-Seq and miRNA analysis
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Our software uses parameters that have been optimized specifically for Ion Torrent data and provides full support for Ion Torrent barcoded data, merge pair data, and paired-end sequence data and has recently significantly enhanced variant call accuracy in Ion Torrent data assemblies.
"The software has been very simple to use. The DNASTAR team is working closely with Life Technologies to simplify the software for the everyday scientist to perform quick and efficient sequence analysis of genes of interest. I’m able to plug raw sequence data from the Ion Torrent server (i.e., FASTQ files) into the software suite and perform SNP analysis, multiple sequence alignments and phylogenetic trees. If I can do this type of bioinformatics, anyone can."
Dr. Luke Daum, co-founder of Longhorn Vaccines & Diagnostics, Inc.
Ion Torrent data is known to have an increased error rate in homopolymeric runs, reducing the accuracy of base calling of heterozygous insertions or deletions in these regions. SeqMan NGen (part of Lasergene Genomics Suite) offers advanced SNP options for users to customize their NGS assembly parameters, including the ability to specify automatic removal of heterozygous indels. This setting addresses the concern with homopolymeric runs and produces the most accurate assembly and variant calling for Ion Torrent data.
Comparative studies of Ion Torrent data with and without heterozygous indel removal illustrate that removal of heterozygous indels greatly decreases the false discovery rate of these assemblies.