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Downloads & Upgrades: Avadis NGS 1.3 beta; Cufflinks 1.3.0; NextGENe


A beta version of Strand's Avadis NGS 1.3 is now available.

The beta release includes an experiment-specific analysis pipeline for small RNA data; COBWeb, a sequence data alignment algorithm based on the Burrows-Wheeler transform that is designed for gapped alignment of DNA and small RNA reads in FASTA and FASTQ files; and three new RNA-seq quantification and normalization options, among other capabilities.

Cufflinks 1.3.0 is available here.

The release includes improvements to the accuracy of Cuffdiff's isoform switching tests and fixes several bugs.

SoftGenetics has added an assembler for Life Technologies' Ion Torrent PGM sequencer to version 2.2 of its NextGENe software.

The "flow-based" assembler, dubbed Floton, treats homopolymer errors as substitution errors and corrects them during the assembly process. It also condenses sequences into flow calls of individual bases and condenses the number of bases in each flow so that insertions and deletions are converted into substitution errors, which improves the assembly.

The Scan

Harvard Team Report One-Time Base Editing Treatment for Motor Neuron Disease in Mice

A base-editing approach restored SMN levels and improved motor function in a mouse model of spinal muscular atrophy, a new Science paper reports.

International Team Examines History of North American Horses

Genetic and other analyses presented in Science find that horses spread to the northern Rockies and Great Plains by the first half of the 17th century.

New Study Examines Genetic Dominance Within UK Biobank

Researchers analyze instances of genetic dominance within UK Biobank data, as they report in Science.

Cell Signaling Pathway Identified as Metastasis Suppressor

A new study in Nature homes in on the STING pathway as a suppressor of metastasis in a mouse model of lung cancer.