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Downloads & Upgrades: PacBio Software; UCSC Browser; Pedant Cloud Service; and More

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Pacific Biosciences said this week that customers of its Single Molecule Real Time sequencer now have access to a number of informatics analysis options and laboratory information management systems through its partner program. These include:

• The BG7 Bacterial Genome Annotation Service from Era7 Bioinformatics, which handles gene and RNA predictions from PacBio de novo assemblies.

Exemplar LIMS from Sapio Sciences, which offers pre-loaded PacBio protocols as well as a workflow-driven architecture and plugin framework for automating sample preparation through sequencing and analysis.

GenoLogics LIMS, which provides preconfigured workflows for the PacBio RS system.

CLC Genomics Workbench and CLC Genomics Server from CLC Bio, which includes tools to call SNPs and perform tertiary analysis of PacBio data.

Partek Flow, which provides tools for quality control, variant detection and copy number analysis, and visualization of aligned PacBio reads.

DNAStar's SeqManNGen, which offers reference-based alignment of PacBio data and SNP calling. Additionally, SeqMan NGen integrates PacBio data with data from other sequencing platforms for integrated sequence assembly projects.

SNP & Variation Suite 7 from Golden Helix, which provides tools for variant classification, filtering, functional annotation, visualization, and statistical analysis for uncovering genotype/phenotype associations or causal variants based on PacBio variant calls.


The Genome Browser group at the University of California, Santa Cruz, has released four tracks for the human assembly derived from the National Center for Biotechnology Information's dbSNP build 135.

The new tracks contain additional annotation data not included in previous dbSNP tracks as well as coloring and filtering options.

The group has also released four tracks for dbSNP build 132, which contain mappings of reference SNPs to the human assembly,


This week, Biomax launched the Pedant Cloud Service to offer the company's Pedant-Pro sequence analysis suite as an online subscription-based service.
The service is available for analyzing bacterial and fungal nucleotide sequences.


Ingenuity has released Ingenuity Variant Analysis, a web-based application for identifying causal variants from human resequencing data (BI 1/13/2012).


Eureka Genomics now offers a 16S metagenomics analysis service.
The service includes algorithms to analyze multiplex samples and to perform quality filtering, clustering, and classification of data. The service will support research into the human microbiome, biofuels, industrial enzymes, microbial genomics, bioremediation, crop protection, comparative population biology, microbial oil recovery, and disease-associated pathogen discovery.


Oxford Gene Technology has launched a bioinformatics analysis service that will support next-generation sequencing-based studies into rare diseases

The service will use the company's proprietary analysis software to help investigators and clinicians identify causative mutations in their data. The company will provide customers with reports that identify affected genes and proteins and suggest possible disease associations with links to additional information on external databases.


This week, BioTeam released MiniLIMS, a laboratory information management system for Life Technologies' Ion Torrent Personal Genome Machine.

The software connects directly to the Ion Torrent Server software, enabling automated data transfer and data processing. It includes capabilities to customize data entry and display to match samples, reagents, workflows, and instruments; as well as to create custom reports


Interactive Biosoftware has released an upgraded version of Alamut, the company's genomic mutation interpretation software.


The National Center for Biotechnology Information has released GenBank 188.0 via ftp

Uncompressed 188.0 flatfiles require roughly 539 gigabytes for sequence files only or 580 gigabytes to include short directory, index, and text files. The ASN.1 data requires approximately 442 gigabytes.


Golden Helix has released SNP & Variation Suite 7.6, the latest version of the company's software for managing, analyzing, and visualizing genomic data.
The updated suite lets uses perform family-based NGS analyses and identify inheritance patterns and recessive traits as well as use reference genomes for testing, filtering, recoding, and statistics based on reference/alternate classification from a public source among other changes.


The Scan

White-Tailed Deer Harbor SARS-CoV-2 Variants No Longer Infecting Humans, Study Finds

A new study in PNAS has found that white-tailed deer could act as a reservoir of SARS-CoV-2 variants no longer found among humans.

Study Points to Benefits of Local Consolidative Therapy, Targeted Treatments in Cancer Care

In JCO Precision Oncology, researchers report that local consolidative therapy combined with molecularly targeted treatments could improve survival for some lung cancer patients.

Genetic Variants That Lower LDL Cholesterol Linked to Reduced Heart Disease Risk

Rare variants in two genes that lower LDL cholesterol are also associated with a decreased risk of coronary heart disease, according to a new JAMA Cardiology study.

Study Links Evolution of Longevity, Social Organization in Mammals

With the help of comparative phylogenetics and transcriptomics, researchers in Nature Communications see ties between lifespan and social organization in mammals.