SeqMan NGen

Application data
Biological application domain(s)	Genomics, Sequence assembly (de novo assembly), Sequence assembly (de-novo assembly), Transcriptome assembly, Whole genome resequencing, SNP detection, Indel detection, ChIP-seq, RNA-Seq alignment
Principal bioinformatics method(s)	Read mapping, Sequence assembly, Sequence alignment
Technology	Ion Torrent, Roche 454, Pacific Biosciences, Illumina, Sanger
Created at	http://www.DNASTAR.com
Maintained?	Yes
Input format(s)	FASTA, FASTQ, Scarf, SFF, SQD, ACE, PHD, ABI, AB1, GFF, CSFASTA/CSQUAL (ABI SOLiD), SCF, TXT, GenBank, SEQ
Output format(s)	BAM, SAM, SQD, ACE, FASTA
Licence	Commercial
Operating system(s)	Windows 7 64-bit or Higher, Mac OS X 10.7, 10.8, or 10.9, Linux Ubuntu 12.04, Linux CentOS 6.5

Summary: Sequence assembly software using traditional and next-gen techonologies. Subsequent analysis of the assembly, including variant discovery, coverage evaluation and consensus annotation is provided through full integration with Lasergene.

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SeqMan NGen® is next-gen sequence assembly software that uses a patented algorithm to provide fast and accurate sequence assembly of data from all major next-gen platforms, including Illumina, Pacific Biosciences, Roche 454, and Ion Torrent. SeqMan NGen represents a breakthrough in sequence assembly software as it has the ability to assemble any size genome quickly and easily on a desktop computer. Optimized assembly parameter settings are automatically determined for you, based on your read technology and your specific project objective, such as genome assembly, targeted resequencing, and de novo transcriptome workflows.

SeqMan NGen is fully integrated with Lasergene's SeqMan Pro, so that once your assembly is complete, numerous tools are available for analyzing your project, including variant and genotype calling using Bayesian statistical models, direct comparison to dbNSFP, dbSNP, COSMIC, and GERP databases during assembly, coverage evaluation, and consensus annotation.

Links

• SeqMan NGen Homepage [ edit link ]

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References

1. . 2010. BMC Genomics
2. . 2011. BMC Genomics
3. . 2012. BMC Genomics
4. . 2012. PNAS
5. . 2012. Journal of Bacteriology
6. . 2012. Systematic biology
7. . 2012. Microbiology
8. . 2012. Proceedings: Biological Sciences / The Royal Society
9. . 2012. Clinical and Vaccine Immunology
10. . 2012. Journal of Bacteriology
11. . 2012. PLoS One
12. . 2012. Journal of Bacteriology
13. . 2012. Applied Environmental Microbiology
14. . 2012. Journal of Bacteriology
15. . 2013. Genetics
16. . 2013. Applied and Environmental Microbiology
17. . 2013. Genome biology and evolution

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