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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

Pfizer-BioNTech Seek Full Vaccine Approval

According to the New York Times, Pfizer and BioNTech are seeking full US Food and Drug Administration approval for their SARS-CoV-2 vaccine.

Viral Integration Study Critiqued

Science writes that a paper reporting that SARS-CoV-2 can occasionally integrate into the host genome is drawing criticism.

Giraffe Species Debate

The Scientist reports that a new analysis aiming to end the discussion of how many giraffe species there are has only continued it.

Science Papers Examine Factors Shaping SARS-CoV-2 Spread, Give Insight Into Bacterial Evolution

In Science this week: genomic analysis points to role of human behavior in SARS-CoV-2 spread, and more.